Is there a way with biopython to obtain the full abstract from a pubmed article?
biopython, pubmed, python
Solution
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.
Problem
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?