Class Bio::Reference
In: lib/bio/reference.rb
Parent: Object

DESCRIPTION

A class for journal reference information.

USAGE

   hash = {'authors' => [ "Hoge, J.P.", "Fuga, F.B." ],
           'title' => "Title of the study.",
           'journal' => "Theor. J. Hoge",
           'volume' => 12,
           'issue' => 3,
           'pages' => "123-145",
           'year' => 2001,
           'pubmed' => 12345678,
           'medline' => 98765432,
           'abstract' => "Hoge fuga. ...",
           'url' => "http://example.com",
           'mesh' => [],
           'affiliations' => []}
   ref = Bio::Reference.new(hash)

   # Formats in the BiBTeX style.
   ref.format("bibtex")

   # Short-cut for Bio::Reference#format("bibtex")
   ref.bibtex

Methods

bibitem   bibtex   cell   current   embl   endnote   format   general   genome_biol   genome_res   nar   nature   new   pubmed_url   rd   science   trends  

Attributes

abstract  [R]  Abstract text in String.
affiliations  [R]  Affiliations in an Array.
authors  [R]  Author names in an Array, [ "Hoge, J.P.", "Fuga, F.B." ].
comments  [R]  Comments for the reference (typically Array of String, or nil)
doi  [R]  DOI identifier (typically String, e.g. "10.1126/science.1110418")
embl_gb_record_number  [R]  Sequence number in EMBL/GenBank records
issue  [R]  issue number (typically Fixnum)
journal  [R]  String with journal name
medline  [R]  medline identifier (typically Fixnum)
mesh  [R]  MeSH terms in an Array.
pages  [R]  page range (typically String, e.g. "123-145")
pubmed  [R]  pubmed identifier (typically Fixnum)
sequence_position  [R]  Position in a sequence that this reference refers to
title  [R]  String with title of the study
url  [R]  An URL String.
volume  [R]  volume number (typically Fixnum)
year  [R]  year of publication (typically Fixnum)

Public Class methods

new(hash)

Create a new Bio::Reference object from a Hash of values. Data is extracted from the values for keys:

  • authors - expected value: Array of Strings
  • title - expected value: String
  • journal - expected value: String
  • volume - expected value: Fixnum or String
  • issue - expected value: Fixnum or String
  • pages - expected value: String
  • year - expected value: Fixnum or String
  • pubmed - expected value: Fixnum or String
  • medline - expected value: Fixnum or String
  • abstract - expected value: String
  • url - expected value: String
  • mesh - expected value: Array of Strings
  • affiliations - expected value: Array of Strings 
     hash = {'authors' => [ "Hoge, J.P.", "Fuga, F.B." ],
         'title' => "Title of the study.",
         'journal' => "Theor. J. Hoge",
         'volume' => 12,
         'issue' => 3,
         'pages' => "123-145",
         'year' => 2001,
         'pubmed' => 12345678,
         'medline' => 98765432,
         'abstract' => "Hoge fuga. ...",
         'url' => "http://example.com",
         'mesh' => [],
         'affiliations' => []}
 ref = Bio::Reference.new(hash)

Arguments:

  • (required) hash: Hash
Returns:Bio::Reference object

[Source]

     # File lib/bio/reference.rb, line 133
133:     def initialize(hash)
134:       @authors  = hash['authors'] || [] # [ "Hoge, J.P.", "Fuga, F.B." ]
135:       @title    = hash['title']   || '' # "Title of the study."
136:       @journal  = hash['journal'] || '' # "Theor. J. Hoge"
137:       @volume   = hash['volume']  || '' # 12
138:       @issue    = hash['issue']   || '' # 3
139:       @pages    = hash['pages']   || '' # 123-145
140:       @year     = hash['year']    || '' # 2001
141:       @pubmed   = hash['pubmed']  || '' # 12345678
142:       @medline  = hash['medline'] || '' # 98765432
143:       @doi      = hash['doi']
144:       @abstract = hash['abstract'] || '' 
145:       @url      = hash['url']
146:       @mesh     = hash['mesh'] || []
147:       @embl_gb_record_number = hash['embl_gb_record_number'] || nil
148:       @sequence_position = hash['sequence_position'] || nil
149:       @comments  = hash['comments']
150:       @affiliations = hash['affiliations'] || []
151:     end

Public Instance methods

bibitem(item = nil)

Returns reference formatted in the bibitem style 

  # ref is a Bio::Reference object
  puts ref.bibitem

    \bibitem{PMID:12345678}
    Hoge, J.P., Fuga, F.B.
    Title of the study.,
    {\em Theor. J. Hoge}, 12(3):123--145, 2001.

Arguments:

  • (optional) item: label string (default: "PMID:#{pubmed}").
Returns:String

[Source]

     # File lib/bio/reference.rb, line 292
292:     def bibitem(item = nil)
293:       item  = "PMID:#{@pubmed}" unless item
294:       pages = @pages.sub('-', '--')
295:       return "\\\\bibitem{\#{item}}\n\#{@authors.join(', ')}\n\#{@title},\n{\\\\em \#{@journal}}, \#{@volume}(\#{@issue}):\#{pages}, \#{@year}.\n".enum_for(:each_line).collect {|line| line.strip}.join("\n")
296:     end
bibtex(section = nil, label = nil, keywords = {})

Returns reference formatted in the BiBTeX style. 

  # ref is a Bio::Reference object
  puts ref.bibtex

    @article{PMID:12345678,
      author  = {Hoge, J.P. and Fuga, F.B.},
      title   = {Title of the study.},
      journal = {Theor. J. Hoge},
      year    = {2001},
      volume  = {12},
      number  = {3},
      pages   = {123--145},
    }

  # using a different section (e.g. "book")
  # (but not really configured for anything other than articles)
  puts ref.bibtex("book")

    @book{PMID:12345678,
      author  = {Hoge, J.P. and Fuga, F.B.},
      title   = {Title of the study.},
      journal = {Theor. J. Hoge},
      year    = {2001},
      volume  = {12},
      number  = {3},
      pages   = {123--145},
    }

Arguments:

  • (optional) section: BiBTeX section as String
  • (optional) label: Label string cited by LaTeX documents. 
                        Default is <tt>"PMID:#{pubmed}"</tt>.
  • (optional) keywords: Hash of additional keywords, 
                           e.g. { 'abstract' => 'This is abstract.' }.
                       You can also override default keywords.
                       To disable default keywords, specify false as
                       value, e.g. { 'url' => false, 'year' => false }.
Returns:String

[Source]

     # File lib/bio/reference.rb, line 343
343:     def bibtex(section = nil, label = nil, keywords = {})
344:       section = "article" unless section
345:       authors = authors_join(' and ', ' and ')
346:       thepages = pages.to_s.empty? ? nil : pages.sub(/\-/, '--')
347:       unless label then
348:         label = "PMID:#{pubmed}"
349:       end
350:       theurl = if !(url.to_s.empty?) then
351:                  url
352:                elsif pmurl = pubmed_url and !(pmurl.to_s.empty?) then
353:                  pmurl
354:                else
355:                  nil
356:                end
357:       hash = {
358:         'author'  => authors.empty?    ? nil : authors,
359:         'title'   => title.to_s.empty? ? nil : title,
360:         'number'  => issue.to_s.empty? ? nil : issue,
361:         'pages'   => thepages,
362:         'url'     => theurl
363:       }
364:       keys = %w( author title journal year volume number pages url )
365:       keys.each do |k|
366:         hash[k] = self.__send__(k.intern) unless hash.has_key?(k)
367:       end
368:       hash.merge!(keywords) { |k, v1, v2| v2.nil? ? v1 : v2 }
369:       bib = [ "@#{section}{#{label}," ]
370:       keys.concat((hash.keys - keys).sort)
371:       keys.each do |kw|
372:         ref = hash[kw]
373:         bib.push "  #{kw.ljust(12)} = {#{ref}}," if ref
374:       end
375:       bib.push "}\n"
376:       return bib.join("\n")
377:     end
cell()

Returns reference formatted in the CELL Press style. 

  # ref is a Bio::Reference object
  puts ref.cell

    Hoge, J.P. and Fuga, F.B. (2001). Title of the study. Theor. J. Hoge 12, 123-145.
Returns:String

[Source]

     # File lib/bio/reference.rb, line 537
537:     def cell
538:       authors = authors_join(' and ')
539:       "#{authors} (#{@year}). #{@title} #{@journal} #{@volume}, #{pages}."
540:     end
current()

Returns reference formatted in the Current Biology (current-biology.com) style. (Same as the Genome Biology style) 

  # ref is a Bio::Reference object
  puts ref.current

    Hoge JP, Fuga FB: Title of the study. Theor J Hoge 2001, 12:123-145.
Returns:String

[Source]

     # File lib/bio/reference.rb, line 495
495:     def current 
496:       self.genome_biol
497:     end
embl()

Returns reference formatted in the EMBL style. 

  # ref is a Bio::Reference object
  puts ref.embl

    RP   1-1859
    RX   PUBMED; 1907511.
    RA   Oxtoby E., Dunn M.A., Pancoro A., Hughes M.A.;
    RT   "Nucleotide and derived amino acid sequence of the cyanogenic
    RT   beta-glucosidase (linamarase) from white clover (Trifolium repens L.)";
    RL   Plant Mol. Biol. 17(2):209-219(1991).

[Source]

     # File lib/bio/reference.rb, line 272
272:     def embl
273:       r = self
274:       Bio::Sequence::Format::NucFormatter::Embl.new('').instance_eval {
275:         reference_format_embl(r)
276:       }
277:     end
endnote()

Returns reference formatted in the Endnote style. 

  # ref is a Bio::Reference object
  puts ref.endnote

    %0 Journal Article
    %A Hoge, J.P.
    %A Fuga, F.B.
    %D 2001
    %T Title of the study.
    %J Theor. J. Hoge
    %V 12
    %N 3
    %P 123-145
    %M 12345678
    %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12345678
    %X Hoge fuga. ...
Returns:String

[Source]

     # File lib/bio/reference.rb, line 238
238:     def endnote
239:       lines = []
240:       lines << "%0 Journal Article"
241:       @authors.each do |author|
242:         lines << "%A #{author}"
243:       end
244:       lines << "%D #{@year}" unless @year.to_s.empty?
245:       lines << "%T #{@title}" unless @title.empty?
246:       lines << "%J #{@journal}" unless @journal.empty?
247:       lines << "%V #{@volume}" unless @volume.to_s.empty?
248:       lines << "%N #{@issue}" unless @issue.to_s.empty?
249:       lines << "%P #{@pages}" unless @pages.empty?
250:       lines << "%M #{@pubmed}" unless @pubmed.to_s.empty?
251:       u = @url.empty? ? pubmed_url : @url
252:       lines << "%U #{u}" unless u.empty?
253:       lines << "%X #{@abstract}" unless @abstract.empty?
254:       @mesh.each do |term|
255:         lines << "%K #{term}"
256:       end
257:       lines << "%+ #{@affiliations.join(' ')}" unless @affiliations.empty?
258:       return lines.join("\n")
259:     end
format(style = nil, *options)

Formats the reference in a given style.

Styles:

  1. nil - general
  2. endnote - Endnote
  3. bibitem - Bibitem (option available)
  4. bibtex - BiBTeX (option available)
  5. rd - rd (option available)
  6. nature - Nature (option available)
  7. science - Science
  8. genome_biol - Genome Biology
  9. genome_res - Genome Research
  10. nar - Nucleic Acids Research
  11. current - Current Biology
  12. trends - Trends in *
  13. cell - Cell Press

See individual methods for details. Basic usage is: 

  # ref is Bio::Reference object
  # using simplest possible call (for general style)
  puts ref.format

  # output in Nature style
  puts ref.format("nature")      # alternatively, puts ref.nature

  # output in Nature short style (see Bio::Reference#nature)
  puts ref.format("nature",true) # alternatively, puts ref.nature(true)

Arguments:

  • (optional) style: String with style identifier
  • (optional) options: Options for styles accepting one
Returns:String

[Source]

     # File lib/bio/reference.rb, line 186
186:     def format(style = nil, *options)
187:       case style
188:       when 'embl'
189:         return embl
190:       when 'endnote'
191:         return endnote
192:       when 'bibitem'
193:         return bibitem(*options)
194:       when 'bibtex'
195:         return bibtex(*options)
196:       when 'rd'
197:         return rd(*options)
198:       when /^nature$/i
199:         return nature(*options)
200:       when /^science$/i
201:         return science
202:       when /^genome\s*_*biol/i
203:         return genome_biol
204:       when /^genome\s*_*res/i
205:         return genome_res
206:       when /^nar$/i
207:         return nar
208:       when /^current/i
209:         return current
210:       when /^trends/i
211:         return trends
212:       when /^cell$/i
213:         return cell
214:       else
215:         return general
216:       end
217:     end
general()

Returns reference formatted in a general/generic style. 

  # ref is a Bio::Reference object
  puts ref.general

    Hoge, J.P., Fuga, F.B. (2001). "Title of the study." Theor. J. Hoge 12:123-145.
Returns:String

[Source]

     # File lib/bio/reference.rb, line 387
387:     def general
388:       authors = @authors.join(', ')
389:       "#{authors} (#{@year}). \"#{@title}\" #{@journal} #{@volume}:#{@pages}."
390:     end
genome_biol()

Returns reference formatted in the Genome Biology (genomebiology.com) style. 

  # ref is a Bio::Reference object
  puts ref.genome_biol

    Hoge JP, Fuga FB: Title of the study. Theor J Hoge 2001, 12:123-145.
Returns:String

[Source]

     # File lib/bio/reference.rb, line 480
480:     def genome_biol
481:       authors = @authors.collect {|name| strip_dots(name)}.join(', ')
482:       journal = strip_dots(@journal)
483:       "#{authors}: #{@title} #{journal} #{@year}, #{@volume}:#{@pages}."
484:     end
genome_res()

Returns reference formatted in the Genome Research (genome.org) style. 

  # ref is a Bio::Reference object
  puts ref.genome_res

    Hoge, J.P. and Fuga, F.B. 2001.
      Title of the study. Theor. J. Hoge 12: 123-145.
Returns:String

[Source]

     # File lib/bio/reference.rb, line 509
509:     def genome_res
510:       authors = authors_join(' and ')
511:       "#{authors} #{@year}.\n  #{@title} #{@journal} #{@volume}: #{@pages}."
512:     end
nar()

Returns reference formatted in the Nucleic Acids Reseach (nar.oxfordjournals.org) style. 

  # ref is a Bio::Reference object
  puts ref.nar

    Hoge, J.P. and Fuga, F.B. (2001) Title of the study. Theor. J. Hoge, 12, 123-145.
Returns:String

[Source]

     # File lib/bio/reference.rb, line 523
523:     def nar
524:       authors = authors_join(' and ')
525:       "#{authors} (#{@year}) #{@title} #{@journal}, #{@volume}, #{@pages}."
526:     end
nature(short = false)

Formats in the Nature Publishing Group (www.nature.com) style. 

  # ref is a Bio::Reference object
  puts ref.nature

    Hoge, J.P. & Fuga, F.B. Title of the study. Theor. J. Hoge 12, 123-145 (2001).

  # optionally, output short version
  puts ref.nature(true)  # or puts ref.nature(short=true)

    Hoge, J.P. & Fuga, F.B. Theor. J. Hoge 12, 123-145 (2001).

Arguments:

  • (optional) short: Boolean (default false)
Returns:String

[Source]

     # File lib/bio/reference.rb, line 436
436:     def nature(short = false)
437:       if short
438:         if @authors.size > 4
439:           authors = "#{@authors[0]} et al."
440:         elsif @authors.size == 1
441:           authors = "#{@authors[0]}"
442:         else
443:           authors = authors_join(' & ')
444:         end
445:         "#{authors} #{@journal} #{@volume}, #{@pages} (#{@year})."
446:       else
447:         authors = authors_join(' & ')
448:         "#{authors} #{@title} #{@journal} #{@volume}, #{@pages} (#{@year})."
449:       end
450:     end
pubmed_url()

Returns a valid URL for pubmed records

Returns:String

[Source]

     # File lib/bio/reference.rb, line 565
565:     def pubmed_url
566:       unless @pubmed.to_s.empty?
567:         cgi = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi"
568:         opts = "cmd=Retrieve&db=PubMed&dopt=Citation&list_uids"
569:         return "#{cgi}?#{opts}=#{@pubmed}"
570:       end
571:       ''
572:     end
rd(str = nil)

Return reference formatted in the RD style. 

  # ref is a Bio::Reference object
  puts ref.rd

    == Title of the study.

    * Hoge, J.P. and Fuga, F.B.

    * Theor. J. Hoge 2001 12:123-145 [PMID:12345678]

    Hoge fuga. ...

An optional string argument can be supplied, but does nothing.

Arguments:

  • (optional) str: String (default nil)
Returns:String

[Source]

     # File lib/bio/reference.rb, line 410
410:     def rd(str = nil)
411:       @abstract ||= str
412:       lines = []
413:       lines << "== " + @title
414:       lines << "* " + authors_join(' and ')
415:       lines << "* #{@journal} #{@year} #{@volume}:#{@pages} [PMID:#{@pubmed}]"
416:       lines << @abstract
417:       return lines.join("\n\n")
418:     end
science()

Returns reference formatted in the Science style. 

  # ref is a Bio::Reference object
  puts ref.science

    J.P. Hoge, F.B. Fuga, Theor. J. Hoge 12 123 (2001).
Returns:String

[Source]

     # File lib/bio/reference.rb, line 461
461:     def science
462:       if @authors.size > 4
463:         authors = rev_name(@authors[0]) + " et al."
464:       else
465:         authors = @authors.collect {|name| rev_name(name)}.join(', ')
466:       end
467:       page_from, = @pages.split('-')
468:       "#{authors}, #{@journal} #{@volume} #{page_from} (#{@year})."
469:     end
trends()

Returns reference formatted in the TRENDS style. 

  # ref is a Bio::Reference object
  puts ref.trends

    Hoge, J.P. and Fuga, F.B. (2001) Title of the study. Theor. J. Hoge 12, 123-145
Returns:String

[Source]

     # File lib/bio/reference.rb, line 551
551:     def trends
552:       if @authors.size > 2
553:         authors = "#{@authors[0]} et al."
554:       elsif @authors.size == 1
555:         authors = "#{@authors[0]}"
556:       else
557:         authors = authors_join(' and ')
558:       end
559:       "#{authors} (#{@year}) #{@title} #{@journal} #{@volume}, #{@pages}"
560:     end

[Validate]