Is there anyway to obtain the full abstract from a PUBmed article using bioPython

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Hi guys, I've been working on a college project which involves me querying a pubmed article. This code is able to tell me if the article has an abstract but I can't find any documentation on how to actually return the abstract. Is it possible using biopython? if it isn't is there another way?

Here's my piece of code

from Bio import Entrez
Entrez.email = "kuharrw@hiram.edu"     # Always tell NCBI who you are
handle = Entrez.esearch(db="pubmed", term="bacteria")
record = Entrez.read(handle)
list = record["IdList"]
print len(list)
for index in range(0, len(list)):
    listId = list[index]
    handle = Entrez.esummary(db="pubmed", id=listId)
    record = Entrez.read(handle)
    print index
    print record[0]["Title"]
    print record[0]["HasAbstract"]
Aug 23, 2018 in Python by charlie_brown
• 7,780 points
1,630 views

1 answer to this question.

0 votes

Hey Charlie, it's certainly possible to pull off what you are trying using BioPython. If you can implement this section as mention in the documentation then you should be able to pull it off cheers

link: http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#sec142

answered Aug 23, 2018 by aryya
• 7,440 points

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