module Bio::KEGG::Common::References

   # File lib/bio/db/kegg/common.rb
30 def references
31   unless @data['REFERENCE']
32     ary = []
33     toptag2array(get('REFERENCE')).each do |ref|
34       hash = Hash.new
35       subtag2array(ref).each do |field|
36         case tag_get(field)
37         when /REFERENCE/
38           cmnt = tag_cut(field).chomp
39           if /^\s*PMID\:(\d+)\s*/ =~ cmnt then
40             hash['pubmed'] = $1
41             cmnt = $'
42           end
43           if cmnt and !cmnt.empty? then
44             hash['comments'] ||= []
45             hash['comments'].push(cmnt)
46           end
47         when /AUTHORS/
48           authors = truncate(tag_cut(field))
49           authors = authors.split(/\, /)
50           authors[-1] = authors[-1].split(/\s+and\s+/) if authors[-1]
51           authors = authors.flatten.map { |a| a.sub(',', ', ') }
52           hash['authors'] = authors
53         when /TITLE/
54           hash['title']   = truncate(tag_cut(field))
55         when /JOURNAL/
56           journal = truncate(tag_cut(field))
57           case journal
58             # KEGG style
59           when /(.*) (\d*(?:\([^\)]+\))?)\:(\d+\-\d+) \((\d+)\)$/
60             hash['journal'] = $1
61             hash['volume']  = $2
62             hash['pages']   = $3
63             hash['year']    = $4
64             # old KEGG style
65           when /(.*) (\d+):(\d+\-\d+) \((\d+)\) \[UI:(\d+)\]$/
66             hash['journal'] = $1
67             hash['volume']  = $2
68             hash['pages']   = $3
69             hash['year']    = $4
70             hash['medline'] = $5
71             # Only journal name and year are available
72           when /(.*) \((\d+)\)$/
73             hash['journal'] = $1
74             hash['year']    = $2
75           else
76             hash['journal'] = journal
77           end
78         end
79       end
80       ary.push(Reference.new(hash))
81     end
82     @data['REFERENCE'] = ary #.extend(Bio::References::BackwardCompatibility)
83 
84   end
85   @data['REFERENCE']
86 end