How to write a Python code for downloading an abstract from PubMed?

Question

This is the code I have as of now and I have tried multiple different ways to get the correct code but to no avail.

I am using the Biopython module for this.

from Bio.Entrez import efetch

def print_abstract(pmid):
    handle = efetch(db='pubmed', id=pmid, retmode='text', rettype='abstract')
    print handle.read()

I tried the code as listed above along with a few tweaks here and there but nothing seems to be working for a simple query.

Answer 1

Step 1: When using python3, use print() as such:

from Bio.Entrez import efetch
 
def print_abstract(pmid):
    handle = efetch(db='pubmed', id=pmid, retmode='text', rettype='abstract')
    print(handle.read())

Step 2: To make use of NCBI's E-utilities, NCBI requires you to specify your email address with each request. So, specify any email (it doesn't have to be real) as follows:

from Bio import Entrez                                                                                                                                                                                          
Entrez.email = '[email protected]'                                                                                                                                                                          

Step 3: Now you can retrieve an abstract programmatically, for example by running

print_abstract(35312860)

This gives me:

1. Acta Diabetol. 2022 Mar 21. doi: 10.1007/s00592-022-01878-z. [Epub ahead of 
print]                                                                                                   
                                                                                                         
Significant and persistent improvements in time in range and positive emotions in
children and adolescents with type 1 diabetes using a closed-loop control system 
after attending a virtual educational camp.                                                              
...
OBJECTIVE: To evaluate the six-month impact of the advanced automated functions...