fetch_pubmed_citation.py

# Takes a PubMed ID (PMID) and your email and returns
# a citation more or less in Vancouver style.
# 
# Depends on biopython:
# $ pip install biopython
# 

def citation(PMID, email):
  from Bio import Entrez
  Entrez.email = email
  handle = Entrez.efetch(db="pubmed", id=PMID, retmode="xml")
  data = Entrez.read(handle)
  article_data = data[0]["MedlineCitation"]["Article"]
  journal_data = article_data["Journal"]
  journal_issue_data = journal_data["JournalIssue"]
  authors = []
  for author in article_data["AuthorList"]:
    author_name = ''
    try:
      author_name = author["LastName"]
    except KeyError:
      continue
    try:
      author_name += ' ' + author["Initials"]
    except KeyError:
      pass
    authors.append(author_name)
  cite = {
    "journal":  str(journal_data["ISOAbbreviation"]),
    "volume": str(journal_issue_data["Issue"]),
    "issue": str(journal_issue_data["Volume"]),
    "month": str(journal_issue_data["PubDate"]["Month"]),
    "year": str(journal_issue_data["PubDate"]["Year"]),
    # remove trailing period after a title if it already exists
    "title": str(article_data["ArticleTitle"]).rstrip("."),
    "authors": ", ".join(authors),
    "pagination": str(article_data["Pagination"]["MedlinePgn"]),
  }
  return "{authors}. {title}. {journal}. {year} {month};{volume}({issue}):{pagination}.".format(**cite)