pubmed_extract_reference.rb

#!/usr/local/bin ruby

# From Paulo Nuin
# Source: http://ruby.genedrift.org/?p=18

require 'rubygems'
require 'bio'

my_file = File.new(ARGV[0])
refs = my_file.readlines
ids = []

refs.each do |line|
  pmid = line.strip().split("\t")
  ids.push(pmid[2])
end

ids.each do |id|
   entry = Bio::PubMed.query(id)
   medline = Bio::MEDLINE.new(entry)
   reference = medline.reference
   puts reference.endnote
end