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

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"]

Suggestion : 2

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?,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,Combined mean and standard deviation from a collection of NumPy arrays of different shapes 3 days ago, Is there anyway to obtain the full abstract from...

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"]

Suggestion : 3

ELink checks for the existence of an external or Related Articles link from a list of one or more primary IDs; retrieves IDs and relevancy scores for links to Entrez databases or Related Articles; creates a hyperlink to the primary LinkOut provider for a specific ID and database, or lists LinkOut URLs and attributes for multiple IDs.,elink Checks for the existence of an external or Related Articles link from a list of one or more primary IDs. Retrieves primary IDs and relevancy scores for links to Entrez databases or Related Articles; creates a hyperlink to the primary LinkOut provider for a specific ID and database, or lists LinkOut URLs and Attributes for multiple IDs.,EInfo provides field names, index term counts, last update, and available links for each Entrez database.,esearch Searches and retrieves primary IDs (for use in EFetch, ELink, and ESummary) and term translations and optionally retains results for future use in the user’s environment.

>>> from Bio
import Entrez
   >>>
   Entrez.email = "Your.Name.Here@example.org" >>>
   handle = Entrez.einfo() # or esearch, efetch, ...
   >>>
   record = Entrez.read(handle) >>>
   handle.close()

>>> handle = Entrez.esummary(db = "pubmed", id = "19304878,14630660", retmode = "xml") >>>
   records = Entrez.parse(handle) >>>
   for record in records:
   ...# each record is a Python dictionary or list.
   ...print(record['Title'])
Biopython: freely available Python tools
for computational molecular biology and bioinformatics.
PDB file parser and structure class implemented in Python. >>>
   handle.close()

>>> from Bio
import Entrez
   >>>
   Entrez.email = "Your.Name.Here@example.org" >>>
   handle = Entrez.efetch(db = "nucleotide", id = "AY851612", rettype = "gb", retmode = "text") >>>
   print(handle.readline().strip())
LOCUS AY851612 892 bp DNA linear PLN 10 - APR - 2007 >>>
   handle.close()

>>> from Bio
import Entrez
   >>>
   Entrez.email = "Your.Name.Here@example.org" >>>
   handle = Entrez.esearch(db = "nucleotide", retmax = 10, term = "opuntia[ORGN] accD", idtype = "acc") >>>
   record = Entrez.read(handle) >>>
   handle.close() >>>
   int(record["Count"]) >= 2
True
   >>>
   "EF590893.1" in record["IdList"]
True
   >>>
   "EF590892.1" in record["IdList"]
True

>>> from Bio
import Entrez
   >>>
   Entrez.email = "Your.Name.Here@example.org" >>>
   pmid = "19304878" >>>
   handle = Entrez.elink(dbfrom = "pubmed", id = pmid, linkname = "pubmed_pubmed") >>>
   record = Entrez.read(handle) >>>
   handle.close() >>>
   print(record[0]["LinkSetDb"][0]["LinkName"])
pubmed_pubmed
   >>>
   linked = [link["Id"]
      for link in record[0]["LinkSetDb"][0]["Link"]
   ] >>>
   "17121776" in linked
True

>>> from Bio
import Entrez
   >>>
   Entrez.email = "Your.Name.Here@example.org" >>>
   record = Entrez.read(Entrez.einfo()) >>>
   'pubmed' in record['DbList']
True

Suggestion : 4

Using the NCBI E-utilities (Entrez Programming Utilities, https://www.ncbi.nlm.nih.gov/books/NBK25499/), you can retrieve and download abstracts associated with a PubMed search without having to sift through the user interface. Even better, this tool doesn’t require any software–its completely URL based. You craft "search" and "fetch" commands as URLs and open them in your browser window to access the abstracts.,Sayers E. The E-utilities In-Depth: Parameters, Syntax and More. 2009 May 29. In: Entrez Programming Utilities Help. Bethesda (MD): National Center for Biotechnology Information (US); 2010-.Available from: http://www.ncbi.nlm.nih.gov/books/NBK25499/,Here, I have shown you how to use the NCBI E-utilities esearch and efetch to download abstracts from PubMed, as well as how to write a Python script to batch download all abstracts corresponding to a keyword search.,http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi? is the backbone of the esearch function.

import csv
import re
import urllib
from time
import sleep

query = 'P2RY8'

# common settings between esearch and efetch
base_url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/'
db = 'db=pubmed'

# esearch specific settings
search_eutil = 'esearch.fcgi?'
search_term = '&term=' + query
search_usehistory = '&usehistory=y'
search_rettype = '&rettype=json'

search_url = base_url + search_eutil + db + search_term + search_usehistory + search_rettype
print(search_url)

http: //eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=P2RY8&usehistory=y&rettype=json

f = urllib.request.urlopen(search_url)
search_data = f.read().decode('utf-8')

search_data