Can Biopython Entrez pull full Pubmed articles from a list of PMIDs?

Question

I've been reading documentation and testing Entrez functions for the last 2 days, and I have it working so that it pulls Abstracts just fine from PMIDs.

But I can't find a clear yes/no answer on if Entrez can pull a text version of the Full Article body, instead of just the abstract field.

I think I might be missing something on the XML parsing, and just need a little clarification because I haven't been able to find it in the documentation. Thanks very much for any assistance.

Answer 1

It cannot extract the full article text (or pdf). You could try to download a pdf through metapub. If you want just text, you can extract it via textract.

import metapub
from urllib.request import urlretrieve
import textract

pmid = '20147967'

url = metapub.FindIt(pmid).url

urlretrieve(url, any_path)

with open(another_path, "w") as textfile:
    textfile.write(textract.process(
        any_path,
        extension='pdf',
        method='pdftotext',
        encoding="utf_8",
    ))