Find the author that published the most papers on Drosophila virilis.



In [1]:

    
from Bio import Entrez
import re

We first want to know now many publications have D. virilis in their title or abstract. We use the NCBI history function in order to refer to this search in our subsequent efetch call.



In [2]:

    
# Remember to edit the e-mail address
Entrez.email = "your_name@yourmailhost.com" # Always tell NCBI who you are
handle = Entrez.esearch(db="pubmed", term="Drosophila virilis[Title/Abstract]", usehistory="y")
record = Entrez.read(handle)
# generate a Python list with all Pubmed IDs of articles about D. virilis
id_list = record["IdList"]
record["Count"]









    Out[2]:





'528'



In [3]:

    
webenv = record["WebEnv"]
query_key = record["QueryKey"]

Retrieve the PubMed entries using our search history



In [4]:

    
handle = Entrez.efetch(db="pubmed",rettype="medline", retmode="text", retstart=0,
retmax=528, webenv=webenv, query_key=query_key)



In [5]:

    
out_handle = open("D_virilis_pubs.txt", "w")
data = handle.read()
handle.close()
out_handle.write(data)
out_handle.close()

We construct a dictionary with all authors as keys and author occurance as value.



In [6]:

    
with open("D_virilis_pubs.txt") as datafile:
    author_dict = {}
    for line in datafile:
        if re.match("AU", line):
            # capture author
            author = line.split("-", 1)[1]
            # remove leading and trailing whitespace
            author = author.strip()
            # if key is present, add 1
            # if it's not present, initialize at 1
            author_dict[author] = 1 + author_dict.get(author, 0)

Dictionaries do not have a natural order but we can sort a dictionary based on the values.



In [7]:

    
# use the values (retrieved by author_dict.get) for sorting the dictionary
# The function "sorted" returns a list that can be indexed to return only some elements, e.g. top 5
for author in sorted(author_dict, key = author_dict.get, reverse = True)[:5]:
    print(author, ":", author_dict[author])









    



Gruntenko NE : 36
Evgen'ev MB : 29
Raushenbakh IIu : 24
Hoikkala A : 23
Korochkin LI : 22