# 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'])) |
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Should the Line 32, 33 be changed into: |
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@ThitherShore is correct - I can verify that suggested fix makes this gist functional. |
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@hongtao510 we download 100 articles in an infinite loop. We see no blocking info since one week. |
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Please update code with ThitherShore's comment. |
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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? |
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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, |
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@ThitherShore is correct we should use |
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for line 36
|
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I get abstracts and not the full text. Any reason why? |
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Pubmed does not contain full texts of papers. Abstracts only |
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How may I save the result in CSV, with Title and Abstract columns? |
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Quick question: is there a extra ")" (or missing "(" in line 39? #edited for formatting |
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@MLZTazim - I'm in the same boat: learning how to use python to drive json to the result. Good fun! |
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@sidewinder02139 the syntax is correct: note the first ")" on that line is part of the output string |
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DOH! LOL |
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ThitherShore is correct. Your code wont work until you enumerate papers['PubmedArticle'] While were at it the last line doesn't work either for the same reason, should be: |
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@jajkelle Updated (better late than never), thank you all for pointing it out |
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Have you encountered the issue that the server will cut you off after querying ~2000 IDs?