Using the translation table from the Jabref program, finds and replaces all scientific journal names to their standardized abbreviated form. First argument is the file to be processed; outputs safely to 'abbreviated.bib'

Abbreviate Journal Names in Bibtex Database.py

#!/usr/bin/env python
#-*- coding: utf-8 -*-
# Supporting Python 3 

import sys, os, re

try:    bibtexdb = open(sys.argv[1]).read()
except: print("Error: specify the file to be processed!")

if not os.path.isfile('journalList.txt'):
    import urllib
    urllib.urlretrieve("https://raw.githubusercontent.com/JabRef/jabref/master/src/main/resources/journals/journalList.txt", 
            filename="journalList.txt")
rulesfile = open('journalList.txt')

for rule in rulesfile.readlines()[::-1]:           ## reversed alphabetical order matches extended journal names first
    pattern1, pattern2 = rule.strip().split(" = ")
    if pattern1 != pattern1.upper() and (' ' in pattern1):        ## avoid mere abbreviations
        #bibtexdb = bibtexdb.replace(pattern1.strip(), pattern2.strip())    ## problem - this is case sensitive
        repl = re.compile(re.escape(pattern1), re.IGNORECASE)               ## this is more robust, although ca. 10x slower
        (bibtexdb, num_subs) = repl.subn(pattern2, bibtexdb)
        if num_subs > 0:
            print "Replacing '%s' FOR '%s'" % (pattern1, pattern2)

with open('abbreviated.bib', 'w') as outfile:
    outfile.write(bibtexdb)
    print "Bibtex database with abbreviated files saved into 'abbreviated.bib'"

I found @trevismd's python3 version of code after I posted my code so I deleted mine.

Anyway, providing python3 code explicitly will be helpful for people who come up with this gist.

By the way, what is journalList.txt based on? A journal I try to submit to requires to follow ISSN List of Title Word Abbreviations so I want to know that.
It seems the list is based on JabRef.

@FilipDominec, feel free to reuse any part of my contribution.

For my own use, I took the code posted by @arahatashun and updated it to pull the latest version of the JabRef lists, which have moved to abbrv.jabref.org and switched to CSV files. It can be found here, in case anyone is interested.