PubMed API

search.ipynb

# To test :
# Go to https://try.jupyter.org/
# Click on "Python 3" in the up-right "New" menu
# Copy the code into a cell
# Modify the search terms in line 32
# Execute with "Ctrl+Enter"

import sys
!{sys.executable} -m pip install biopython
from Bio import Entrez
import json

def search(query):
    Entrez.email = '[email protected]'
    handle = Entrez.esearch(db='pubmed', 
                            sort='relevance', 
                            retmax='20',
                            retmode='xml', 
                            term=query)
    results = Entrez.read(handle)
    return results

def fetch_details(id_list):
    ids = ','.join(id_list)
    Entrez.email = '[email protected]'
    handle = Entrez.efetch(db='pubmed',
                           retmode='xml',
                           id=ids)
    results = Entrez.read(handle)
    return results

if __name__ == '__main__':
    results = search('carissa spinarum')
    id_list = results['IdList']
    papers = fetch_details(id_list)
    print("")
    print("-------------------------------------------------------------------------------------------------------------------")
    print("RESULTS :")
    print("-------------------------------------------------------------------------------------------------------------------")
    print("")
    for i, paper in enumerate(papers['PubmedArticle']): 
        print("%d) %s" % (i+1, paper['MedlineCitation']['Article']['ArticleTitle']))
        print(json.dumps(paper['MedlineCitation']['Article']['Abstract']['AbstractText'], indent=2, separators=(',', ':')))