A small module to download and convert PubMed citations to TextTile format.

gistfile1.builder

require 'rubygems'
require 'bio'

module PubMed

  # Download and annotate the given pubmed_id and return a citation in textile format.
  # Example Citation: 
  # Smythe MA, Stephens JL, Koerber JM, Mattson JC: A comparison of lepirudin and argatroban outcomes. 
  # Clin Appl Thromb Hemost. 2005 Oct;11(4):371-4. "Pubmed":http://www.ncbi.nlm.nih.gov/pubmed/16244762
  def PubMed.annotate(pubmed_id)
    raise ArgumentError unless pubmed_id.to_i > 0
    citation = ''
    result = Bio::PubMed.pmfetch(pubmed_id)
    raise ArgumentError if result =~ /Error occurred/
    medline = Bio::MEDLINE.new(result)

    if medline.au && !( medline.au.strip.nil? || medline.au.strip == '')
      citation = medline.au.gsub(/\n/, ', ') + ': ' + medline.title + ' ' + medline.source
    elsif !(medline.nil? || medline == '')
      citation = medline.title + ' ' + medline.source
    else
      raise ArgumentError
    end

    citation.gsub!(/\n/, ' ')
    citation.gsub!(/\s{2,}/, ' ')
    citation = "\n# #{citation} \"Pubmed\":http://www.ncbi.nlm.nih.gov/pubmed/#{pubmed_id}"
  end
end