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

Question

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"]

Answer 1

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