Class: Bio::MEDLINE

Inherits:
NCBIDB show all
Defined in:
lib/bio/db/medline.rb

Overview

Description

NCBI PubMed/MEDLINE database class.

Examples

medline = Bio::MEDLINE.new(txt)
medline.reference
medline.pmid == medline.entry_id
medilne.mesh

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods inherited from DB

#exists?, #fetch, #get, open, #tags

Constructor Details

#initialize(entry) ⇒ MEDLINE

Returns a new instance of MEDLINE.



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# File 'lib/bio/db/medline.rb', line 28

def initialize(entry)
  @pubmed = Hash.new('')

  tag = ''
  entry.each_line do |line|
    if line =~ /^\w/
      tag = line[0,4].strip
    else
      # continuation from previous lines
      @pubmed[tag] = @pubmed[tag].sub(/(?:\r|\r\n|\n)\z/, ' ')
    end
    value = line[6..-1]
    @pubmed[tag] += value if value
  end
end

Instance Attribute Details

#pubmed ⇒ Object (readonly)

Returns the value of attribute pubmed.



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# File 'lib/bio/db/medline.rb', line 43

def pubmed
  @pubmed
end

Instance Method Details

#ab ⇒ Object Also known as: abstract

AB - Abstract

Abstract.



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# File 'lib/bio/db/medline.rb', line 145

def ab
  @pubmed['AB'].gsub(/\s+/, ' ').strip
end

#ad ⇒ Object Also known as: affiliations

AD - Affiliation

Institutional affiliation and address of the first author, and grant
numbers.



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# File 'lib/bio/db/medline.rb', line 193

def ad
  @pubmed['AD'].strip.split(/\n/)
end

#au ⇒ Object

AU - Author Name

Authors' names.



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# File 'lib/bio/db/medline.rb', line 152

def au
  @pubmed['AU'].strip
end

#authors ⇒ Object 



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# File 'lib/bio/db/medline.rb', line 156

def authors
  authors = []
  au.split(/\n/).each do |author|
    if author =~ / /
      name = author.split(/\s+/)
      suffix = nil
      if name.length > 2 && name[-2] =~ /^[A-Z]+$/ # second to last are the initials
        suffix = name.pop
      end
      initial = name.pop.split(//).join('. ')
      author = "#{name.join(' ')}, #{initial}."
    end
    if suffix
      author << " " + suffix
    end
    authors.push(author)
  end
  return authors
end

#doi ⇒ Object

AID - Article Identifier

Article ID values may include the pii (controlled publisher identifier)
or doi (Digital Object Identifier).



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# File 'lib/bio/db/medline.rb', line 201

def doi
  @pubmed['AID'][/(\S+) \[doi\]/, 1]
end

#dp ⇒ Object Also known as: date

DP - Publication Date

The date the article was published.



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# File 'lib/bio/db/medline.rb', line 127

def dp
  @pubmed['DP'].strip
end

#ip ⇒ Object Also known as: issue

IP - Issue

The number of the issue, part, or supplement of the journal in which
the article was published.



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# File 'lib/bio/db/medline.rb', line 102

def ip
  @pubmed['IP'].strip
end

#mh ⇒ Object Also known as: mesh

MH - MeSH Terms

NLM's controlled vocabulary.



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# File 'lib/bio/db/medline.rb', line 185

def mh
  @pubmed['MH'].strip.split(/\n/)
end

#pages ⇒ Object 



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# File 'lib/bio/db/medline.rb', line 113

def pages
  pages = pg
  if pages =~ /-/
    from, to = pages.split('-')
    if (len = from.length - to.length) > 0
      to = from[0,len] + to
    end
    pages = "#{from}-#{to}"
  end
  return pages
end

#pg ⇒ Object

PG - Page Number

The full pagination of the article.



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# File 'lib/bio/db/medline.rb', line 109

def pg
  @pubmed['PG'].strip
end

#pii ⇒ Object 



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# File 'lib/bio/db/medline.rb', line 205

def pii
  @pubmed['AID'][/(\S+) \[pii\]/, 1]
end

#pmid ⇒ Object Also known as: entry_id

PMID - PubMed Unique Identifier

Unique number assigned to each PubMed citation.



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# File 'lib/bio/db/medline.rb', line 74

def pmid
  @pubmed['PMID'].strip
end

#pt ⇒ Object Also known as: publication_type

PT - Publication Type

The type of material the article represents.



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# File 'lib/bio/db/medline.rb', line 278

def pt
  @pubmed['PT'].strip.split(/\n/)   
end

#reference ⇒ Object

returns a Reference object.



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# File 'lib/bio/db/medline.rb', line 47

def reference
  hash = Hash.new

  hash['authors']	= authors
  hash['title']	= title
  hash['journal']	= journal
  hash['volume']	= volume
  hash['issue']	= issue
  hash['pages']	= pages
  hash['year']	= year
  hash['pubmed']	= pmid
  hash['medline']  	= ui
  hash['abstract']	= abstract
  hash['mesh']	= mesh
  hash['doi']	= doi
  hash['affiliations'] = affiliations

  hash.delete_if { |k, v| v.nil? or v.empty? }

  return Reference.new(hash)
end

#so ⇒ Object Also known as: source

SO - Source

Composite field containing bibliographic information.



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# File 'lib/bio/db/medline.rb', line 178

def so
  @pubmed['SO'].strip
end

#ta ⇒ Object Also known as: journal

TA - Journal Title Abbreviation

Standard journal title abbreviation.



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# File 'lib/bio/db/medline.rb', line 87

def ta
  @pubmed['TA'].gsub(/\s+/, ' ').strip
end

#ti ⇒ Object Also known as: title

TI - Title Words

The title of the article.



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# File 'lib/bio/db/medline.rb', line 138

def ti
  @pubmed['TI'].gsub(/\s+/, ' ').strip
end

#ui ⇒ Object

UI - MEDLINE Unique Identifier

Unique number assigned to each MEDLINE citation.



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# File 'lib/bio/db/medline.rb', line 81

def ui
  @pubmed['UI'].strip
end

#vi ⇒ Object Also known as: volume

VI - Volume

Journal volume.



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# File 'lib/bio/db/medline.rb', line 94

def vi
  @pubmed['VI'].strip
end

#year ⇒ Object 



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# File 'lib/bio/db/medline.rb', line 132

def year
  dp[0,4]
end