Small script to retrieve data of all publications of a given journal in a given time frame from MEDLINE

medline_search.py

#!/usr/bin/python 

# medline_search.py
#
# Small script to retrieve data of all publications of a given journal in
# a given time frame from MEDLINE
#
# 2014 - Konrad Förstner <[email protected]>
#
#  To the extent possible under law, the author have dedicated all
#  copyright and related and neighboring rights to this software to
#  the public domain worldwide. This software is distributed without
#  any warranty.
#
# See <http://creativecommons.org/publicdomain/zero/1.0/>
#
# MEDLINE/PubMed Data Element (Field) Descriptions can be found at 
# http://www.nlm.nih.gov/bsd/mms/medlineelements.html
#
# Version 1.0


from Bio import Entrez
from Bio import Medline

search_term = '"Mol Microbiol"[jour] 2013/05:2014/11 [edat]'
output_file = "medline_search_result.csv"
email = "[email protected]"
max_number_of_hits = 500

Entrez.email = email
esearch = Entrez.esearch(
    db='pubmed', term=search_term, retmax=max_number_of_hits, )
hits = Entrez.read(esearch)

with open(output_file, "w") as output_fh:
    output_fh.write(
        "\t".join(
            ["Title",  "Abstract", "Authors", "Affiliation", "Entrez time",
             "Date create", "Source", "Publication Type", "DOI", "Pubmed ID"]) 
        + "\n")
    for pmid in hits["IdList"]:
        efetch = Entrez.efetch(
            db="pubmed", id=pmid, rettype="medline", retmode="text")
        for record in Medline.parse(efetch):
            output_fh.write(
                "\t".join([
                    record.get("TI", "-"),
                    record.get("AB", "-"),
                    ", ".join(record.get("AU", ["-"])),
                    record.get("AD", "-"),
                    record.get("EDAT", "-"),
                    record.get("DA", "-"),
                    record.get("SO", "-"),
                    ", ".join(record.get("PT", ["-"])),
                    record.get("LID", "-"),
                    record.get("PMID", "-")]) + "\n")