Is there a way with biopython to obtain the full abstract from a pubmed article?

Question

I currently have the following code which queries pubmed:

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"]

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?

score 6 · Accepted Answer · answered Feb 09 '14 at 22:46

6

Yes, it's obviously possible using BioPython. If you follow exactly this section, you should be able to get the abstract from pubmed: http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#sec142

If you don't find this link helpful, please let me know. I will get back to you soon.

answered Feb 09 '14 at 22:46

Sharif Mamun

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Thanks so much, I spent hours today going through that document trying to find it and I must have just missed that section. – Ryan Raten Kuhar Feb 09 '14 at 23:34

Is there a way with biopython to obtain the full abstract from a pubmed article?

1 Answers1