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pmid2bib
executable file
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pmid2bib
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#! /usr/bin/env python3
# Given a single PMID, output a formatted BibTeX entry.
#
# You have to add the citekey yourself, and you may need to do some
# light editing of things that the script isn't smart enough to do.
# Check for accented characters on authornames, and capitalization
# and italics (species names) in titles.
#
# Usage: pmid2bib <pmid>
# Example: pmid2bib 11733745
#
# This is also a good example of parsing XML with
# xml.etree.ElementTree.
import sys
import urllib.request
import xml.etree.ElementTree as ET
if len(sys.argv) != 2:
sys.exit('Usage: pmid2bib <pmid>')
pmid = sys.argv[1]
efetch_url = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id={}&rettype=abstract'.format(pmid);
# Given the XML's "SR" for initials, convert to "S. R." for BibTeX.
def format_author_initials(s):
initials_formatted = []
for c in s: initials_formatted.append('{}.'.format(c))
return ' '.join(initials_formatted)
# Given the XML's "Title with only the first word capitalized",
# capitalize throughout to "Title with Only the First Word
# Capitalized". The style rule is that short prepositions,
# conjunctions, and articles of four or fewer letters are
# uncapitalized; here I do it with a simple list of common ones.
#
# I also try to recognize some common species names to leave
# them uncapitalized, but you'll need to add the \emph{} yourself.
#
# Also, wrap anything with more than one capital letter
# in it (example: "RNA") with {} brackets to protect the
# capitalization in BibTeX.
#
# Python's s.title() method does NOT work for this. It converts
# RNA to Rna, for example.
#
def format_title(s):
nocap = ['a', 'an', 'and', 'as', 'at', 'but', 'by', 'for', 'if', 'in', 'nor', 'of', 'off',
'on', 'or', 'up', 'so', 'the', 'to', 'up', 'via', 'with', 'yet']
common_species = ['cerevisiae', 'coli', 'elegans', 'furiosus', 'melanogaster', 'musculus', 'sapiens']
twords = []
nw = 0
s = s.rstrip('.')
for w in s.split(' '):
nw += 1
extracaps = sum(1 for c in w[1:] if c.isupper())
if extracaps: twords.append('{{{}}}'.format(w))
elif nw == 1: twords.append(w)
elif w[0].isupper(): twords.append('{{{}}}{}'.format(w[0], w[1:]))
elif w in nocap: twords.append(w)
elif w in common_species: twords.append(w)
else: twords.append(w.capitalize())
return ' '.join(twords)
# Given the XML's official ISO abbreviation for the journal, typically
# without any .'s, return the abbreviation that I use. This is just
# an enumerated list of journals, and it's incomplete; I'll add to it
# over time.
#
def format_journal(s):
journal_map = {
'Curr Biol': 'Curr. Biol.',
'Elife': 'eLife',
'Nat Rev Genet': 'Nat. Rev. Genet.',
'Nucleic Acids Res': 'Nucleic Acids Res.',
'PLoS Biol': 'PLOS Biol.',
'PLoS Comput Biol': 'PLOS Comput. Biol.',
'Proc Natl Acad Sci U S A': 'Proc. Natl. Acad. Sci. USA',
}
if s in journal_map: return journal_map[s]
else: return s
# Main body.
# Get the XML text with urllib.request;
# parse it with xml.etree.ElementTree.
#
# To see the XML that's being parsed, go to a browser with e.g.
# https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=11733745&rettype=abstract
#
with urllib.request.urlopen(efetch_url) as response:
body = response.read()
root = ET.fromstring(body)
PubmedArticle = root.find('PubmedArticle')
authors = []
for Author in PubmedArticle.iter('Author'):
author_surname = Author.find('LastName').text
author_initials = format_author_initials(Author.find('Initials').text)
authors.append('{} {}'.format(author_initials, author_surname))
title = PubmedArticle.find('./MedlineCitation/Article/ArticleTitle').text
journal = PubmedArticle.find('./MedlineCitation/Article/Journal/ISOAbbreviation').text
volume = PubmedArticle.find('./MedlineCitation/Article/Journal/JournalIssue/Volume').text
# For single "page numbers" that are really an e-identifier, they can either
# appear as an "ELocationID" of type "pii", or a StartPage without an EndPage.
if PubmedArticle.find('./MedlineCitation/Article/Pagination'):
page_start = PubmedArticle.find('./MedlineCitation/Article/Pagination/StartPage')
page_end = PubmedArticle.find('./MedlineCitation/Article/Pagination/EndPage')
if page_end != None: pages = '{}-{}'.format(page_start.text, page_end.text)
else: pages = '{}'.format(page_start.text)
else:
for eloc in PubmedArticle.findall('./MedlineCitation/Article/ELocationID'):
if (eloc.get('EIdType') == 'pii'): pages = eloc.text
idlist = PubmedArticle.find('./PubmedData/ArticleIdList')
pmcid = None
doi = None
for id in idlist.findall('ArticleId'):
if (id.get('IdType') == 'pmc'): pmcid = id
elif (id.get('IdType') == 'doi'): doi = id
print ('@Article{,')
print (' author = {{{}}},'.format(' and '.join(authors)))
print (' title = {{{}}},'.format(format_title(title)))
print (' journal = {{{}}},'.format(format_journal(journal)))
print (' volume = {},'.format(volume))
print (' pages = {{{}}},'.format(pages))
print (' pmid = {},'.format(pmid))
if pmcid != None: print (' pmcid = {{{}}},'.format(pmcid.text))
if doi != None: print (' reprinturl = {{https://doi.org/{}}},'.format(doi.text))
print ('}')