Class: Bio::Reference

Inherits:
Object show all
Defined in:
lib/bio/reference.rb

Overview

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

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(hash) ⇒ Reference

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



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# File 'lib/bio/reference.rb', line 133

def initialize(hash)
  @authors  = hash['authors'] || [] # [ "Hoge, J.P.", "Fuga, F.B." ]
  @title    = hash['title']   || '' # "Title of the study."
  @journal  = hash['journal'] || '' # "Theor. J. Hoge"
  @volume   = hash['volume']  || '' # 12
  @issue    = hash['issue']   || '' # 3
  @pages    = hash['pages']   || '' # 123-145
  @year     = hash['year']    || '' # 2001
  @pubmed   = hash['pubmed']  || '' # 12345678
  @medline  = hash['medline'] || '' # 98765432
  @doi      = hash['doi']
  @abstract = hash['abstract'] || '' 
  @url      = hash['url']
  @mesh     = hash['mesh'] || []
  @embl_gb_record_number = hash['embl_gb_record_number'] || nil
  @sequence_position = hash['sequence_position'] || nil
  @comments  = hash['comments']
  @affiliations = hash['affiliations'] || []
end

Instance Attribute Details

#abstract ⇒ Object (readonly)

Abstract text in String.



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# File 'lib/bio/reference.rb', line 77

def abstract
  @abstract
end

#affiliations ⇒ Object (readonly)

Affiliations in an Array.



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# File 'lib/bio/reference.rb', line 86

def affiliations
  @affiliations
end

#authors ⇒ Object (readonly)

Author names in an Array, [ “Hoge, J.P.”, “Fuga, F.B.” ].



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# File 'lib/bio/reference.rb', line 47

def authors
  @authors
end

#comments ⇒ Object (readonly)

Comments for the reference (typically Array of String, or nil)



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# File 'lib/bio/reference.rb', line 95

def comments
  @comments
end

#doi ⇒ Object (readonly)

DOI identifier (typically String, e.g. “10.1126/science.1110418”)



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# File 'lib/bio/reference.rb', line 74

def doi
  @doi
end

#embl_gb_record_number ⇒ Object (readonly)

Sequence number in EMBL/GenBank records



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# File 'lib/bio/reference.rb', line 89

def embl_gb_record_number
  @embl_gb_record_number
end

#issue ⇒ Object (readonly)

issue number (typically Fixnum)



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# File 'lib/bio/reference.rb', line 59

def issue
  @issue
end

#journal ⇒ Object (readonly)

String with journal name



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# File 'lib/bio/reference.rb', line 53

def journal
  @journal
end

#medline ⇒ Object (readonly)

medline identifier (typically Fixnum)



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# File 'lib/bio/reference.rb', line 71

def medline
  @medline
end

#mesh ⇒ Object (readonly)

MeSH terms in an Array.



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# File 'lib/bio/reference.rb', line 83

def mesh
  @mesh
end

#pages ⇒ Object (readonly)

page range (typically String, e.g. “123-145”)



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# File 'lib/bio/reference.rb', line 62

def pages
  @pages
end

#pubmed ⇒ Object (readonly)

pubmed identifier (typically Fixnum)



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# File 'lib/bio/reference.rb', line 68

def pubmed
  @pubmed
end

#sequence_position ⇒ Object (readonly)

Position in a sequence that this reference refers to



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# File 'lib/bio/reference.rb', line 92

def sequence_position
  @sequence_position
end

#title ⇒ Object (readonly)

String with title of the study



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# File 'lib/bio/reference.rb', line 50

def title
  @title
end

#url ⇒ Object (readonly)

An URL String.



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# File 'lib/bio/reference.rb', line 80

def url
  @url
end

#volume ⇒ Object (readonly)

volume number (typically Fixnum)



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# File 'lib/bio/reference.rb', line 56

def volume
  @volume
end

#year ⇒ Object (readonly)

year of publication (typically Fixnum)



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# File 'lib/bio/reference.rb', line 65

def year
  @year
end

Instance Method Details

#bibitem(item = nil) ⇒ Object

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



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# File 'lib/bio/reference.rb', line 292

def bibitem(item = nil)
  item  = "PMID:#{@pubmed}" unless item
  pages = @pages.sub('-', '--')
  return <<-"END".enum_for(:each_line).collect {|line| line.strip}.join("\n")
    \\bibitem{#{item}}
    #{@authors.join(', ')}
    #{@title},
    {\\em #{@journal}}, #{@volume}(#{@issue}):#{pages}, #{@year}.
  END
end

#bibtex(section = nil, label = nil, keywords = {}) ⇒ Object

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



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# File 'lib/bio/reference.rb', line 342

def bibtex(section = nil, label = nil, keywords = {})
  section = "article" unless section
  authors = authors_join(' and ', ' and ')
  thepages = pages.to_s.empty? ? nil : pages.sub(/\-/, '--')
  unless label then
    label = "PMID:#{pubmed}"
  end
  theurl = if !(url.to_s.empty?) then
             url
           elsif pmurl = pubmed_url and !(pmurl.to_s.empty?) then
             pmurl
           else
             nil
           end
  hash = {
    'author'  => authors.empty?    ? nil : authors,
    'title'   => title.to_s.empty? ? nil : title,
    'number'  => issue.to_s.empty? ? nil : issue,
    'pages'   => thepages,
    'url'     => theurl
  }
  keys = %w( author title journal year volume number pages url )
  keys.each do |k|
    hash[k] = self.__send__(k.intern) unless hash.has_key?(k)
  end
  hash.merge!(keywords) { |k, v1, v2| v2.nil? ? v1 : v2 }
  bib = [ "@#{section}{#{label}," ]
  keys.concat((hash.keys - keys).sort)
  keys.each do |kw|
    ref = hash[kw]
    bib.push "  #{kw.ljust(12)} = {#{ref}}," if ref
  end
  bib.push "}\n"
  return bib.join("\n")
end

#cell ⇒ Object

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



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# File 'lib/bio/reference.rb', line 536

def cell
  authors = authors_join(' and ')
  "#{authors} (#{@year}). #{@title} #{@journal} #{@volume}, #{pages}."
end

#current ⇒ Object

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



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# File 'lib/bio/reference.rb', line 494

def current 
  self.genome_biol
end

#embl ⇒ Object

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).



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# File 'lib/bio/reference.rb', line 272

def embl
  r = self
  Bio::Sequence::Format::NucFormatter::Embl.new('').instance_eval {
    reference_format_embl(r)
  }
end

#endnote ⇒ Object

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



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# File 'lib/bio/reference.rb', line 238

def endnote
  lines = []
  lines << "%0 Journal Article"
  @authors.each do |author|
    lines << "%A #{author}"
  end
  lines << "%D #{@year}" unless @year.to_s.empty?
  lines << "%T #{@title}" unless @title.empty?
  lines << "%J #{@journal}" unless @journal.empty?
  lines << "%V #{@volume}" unless @volume.to_s.empty?
  lines << "%N #{@issue}" unless @issue.to_s.empty?
  lines << "%P #{@pages}" unless @pages.empty?
  lines << "%M #{@pubmed}" unless @pubmed.to_s.empty?
  u = @url.empty? ? pubmed_url : @url
  lines << "%U #{u}" unless u.empty?
  lines << "%X #{@abstract}" unless @abstract.empty?
  @mesh.each do |term|
    lines << "%K #{term}"
  end
  lines << "%+ #{@affiliations.join(' ')}" unless @affiliations.empty?
  return lines.join("\n")
end

#format(style = nil, *options) ⇒ Object

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



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# File 'lib/bio/reference.rb', line 186

def format(style = nil, *options)
  case style
  when 'embl'
    return embl
  when 'endnote'
    return endnote
  when 'bibitem'
    return bibitem(*options)
  when 'bibtex'
    return bibtex(*options)
  when 'rd'
    return rd(*options)
  when /^nature$/i
    return nature(*options)
  when /^science$/i
    return science
  when /^genome\s*_*biol/i
    return genome_biol
  when /^genome\s*_*res/i
    return genome_res
  when /^nar$/i
    return nar
  when /^current/i
    return current
  when /^trends/i
    return trends
  when /^cell$/i
    return cell
  else
    return general
  end
end

#general ⇒ Object

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



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# File 'lib/bio/reference.rb', line 386

def general
  authors = @authors.join(', ')
  "#{authors} (#{@year}). \"#{@title}\" #{@journal} #{@volume}:#{@pages}."
end

#genome_biol ⇒ Object

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



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# File 'lib/bio/reference.rb', line 479

def genome_biol
  authors = @authors.collect {|name| strip_dots(name)}.join(', ')
  journal = strip_dots(@journal)
  "#{authors}: #{@title} #{journal} #{@year}, #{@volume}:#{@pages}."
end

#genome_res ⇒ Object

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



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# File 'lib/bio/reference.rb', line 508

def genome_res
  authors = authors_join(' and ')
  "#{authors} #{@year}.\n  #{@title} #{@journal} #{@volume}: #{@pages}."
end

#nar ⇒ Object

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



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# File 'lib/bio/reference.rb', line 522

def nar
  authors = authors_join(' and ')
  "#{authors} (#{@year}) #{@title} #{@journal}, #{@volume}, #{@pages}."
end

#nature(short = false) ⇒ Object

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



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# File 'lib/bio/reference.rb', line 435

def nature(short = false)
  if short
    if @authors.size > 4
      authors = "#{@authors[0]} et al."
    elsif @authors.size == 1
      authors = "#{@authors[0]}"
    else
      authors = authors_join(' & ')
    end
    "#{authors} #{@journal} #{@volume}, #{@pages} (#{@year})."
  else
    authors = authors_join(' & ')
    "#{authors} #{@title} #{@journal} #{@volume}, #{@pages} (#{@year})."
  end
end

#pubmed_url ⇒ Object

Returns a valid URL for pubmed records

Returns

String



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# File 'lib/bio/reference.rb', line 564

def pubmed_url
  unless @pubmed.to_s.empty?
    cgi = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi"
    opts = "cmd=Retrieve&db=PubMed&dopt=Citation&list_uids"
    return "#{cgi}?#{opts}=#{@pubmed}"
  end
  ''
end

#rd(str = nil) ⇒ Object

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



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# File 'lib/bio/reference.rb', line 409

def rd(str = nil)
  @abstract ||= str
  lines = []
  lines << "== " + @title
  lines << "* " + authors_join(' and ')
  lines << "* #{@journal} #{@year} #{@volume}:#{@pages} [PMID:#{@pubmed}]"
  lines << @abstract
  return lines.join("\n\n")
end

#science ⇒ Object

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



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# File 'lib/bio/reference.rb', line 460

def science
  if @authors.size > 4
    authors = rev_name(@authors[0]) + " et al."
  else
    authors = @authors.collect {|name| rev_name(name)}.join(', ')
  end
  page_from, = @pages.split('-')
  "#{authors}, #{@journal} #{@volume} #{page_from} (#{@year})."
end

#trends ⇒ Object

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



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# File 'lib/bio/reference.rb', line 550

def trends
  if @authors.size > 2
    authors = "#{@authors[0]} et al."
  elsif @authors.size == 1
    authors = "#{@authors[0]}"
  else
    authors = authors_join(' and ')
  end
  "#{authors} (#{@year}) #{@title} #{@journal} #{@volume}, #{@pages}"
end