Class: Bio::MEDLINE

    # File lib/bio/db/medline.rb, line 28
28:   def initialize(entry)
29:     @pubmed = Hash.new('')
30: 
31:     tag = ''
32:     entry.each_line do |line|
33:       if line =~ /^\w/
34:         tag = line[0,4].strip
35:       end
36:       @pubmed[tag] += line[6..-1] if line.length > 6
37:     end
38:   end

ab()

AB - Abstract

  Abstract.

[Source]

     # File lib/bio/db/medline.rb, line 140
140:   def ab
141:     @pubmed['AB'].gsub(/\s+/, ' ').strip
142:   end

abstract()

Alias for ab

ad()

AD - Affiliation

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

[Source]

     # File lib/bio/db/medline.rb, line 188
188:   def ad
189:     @pubmed['AD'].strip.split(/\n/)
190:   end

affiliations()

Alias for ad

au()

AU - Author Name

  Authors' names.

[Source]

     # File lib/bio/db/medline.rb, line 147
147:   def au
148:     @pubmed['AU'].strip
149:   end

authors()

[Source]

     # File lib/bio/db/medline.rb, line 151
151:   def authors
152:     authors = []
153:     au.split(/\n/).each do |author|
154:       if author =~ / /
155:         name = author.split(/\s+/)
156:         suffix = nil
157:         if name.length > 2 && name[-2] =~ /^[A-Z]+$/ # second to last are the initials
158:           suffix = name.pop
159:         end
160:         initial = name.pop.split(//).join('. ')
161:         author = "#{name.join(' ')}, #{initial}."
162:       end
163:       if suffix
164:         author << " " + suffix
165:       end
166:       authors.push(author)
167:     end
168:     return authors
169:   end

date()

Alias for dp

doi()

AID - Article Identifier

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

[Source]

     # File lib/bio/db/medline.rb, line 196
196:   def doi
197:     @pubmed['AID'][/(\S+) \[doi\]/, 1]
198:   end

dp()

DP - Publication Date

  The date the article was published.

[Source]

     # File lib/bio/db/medline.rb, line 122
122:   def dp
123:     @pubmed['DP'].strip
124:   end

entry_id()

Alias for pmid

ip()

IP - Issue

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

[Source]

    # File lib/bio/db/medline.rb, line 97
97:   def ip
98:     @pubmed['IP'].strip
99:   end

issue()

Alias for ip

journal()

Alias for ta

mesh()

Alias for mh

mh()

MH - MeSH Terms

  NLM's controlled vocabulary.

[Source]

     # File lib/bio/db/medline.rb, line 180
180:   def mh
181:     @pubmed['MH'].strip.split(/\n/)
182:   end

pages()

[Source]

     # File lib/bio/db/medline.rb, line 108
108:   def pages
109:     pages = pg
110:     if pages =~ /-/
111:       from, to = pages.split('-')
112:       if (len = from.length - to.length) > 0
113:         to = from[0,len] + to
114:       end
115:       pages = "#{from}-#{to}"
116:     end
117:     return pages
118:   end

pg()

PG - Page Number

  The full pagination of the article.

[Source]

     # File lib/bio/db/medline.rb, line 104
104:   def pg
105:     @pubmed['PG'].strip
106:   end

pii()

[Source]

     # File lib/bio/db/medline.rb, line 200
200:   def pii
201:     @pubmed['AID'][/(\S+) \[pii\]/, 1]
202:   end

pmid()

PMID - PubMed Unique Identifier

  Unique number assigned to each PubMed citation.

[Source]

    # File lib/bio/db/medline.rb, line 69
69:   def pmid
70:     @pubmed['PMID'].strip
71:   end

pt()

PT - Publication Type

  The type of material the article represents.

[Source]

     # File lib/bio/db/medline.rb, line 273
273:   def pt
274:     @pubmed['PT'].strip.split(/\n/)   
275:   end

publication_type()

Alias for pt

reference()

returns a Reference object.

[Source]

    # File lib/bio/db/medline.rb, line 43
43:   def reference
44:     hash = Hash.new('')
45: 
46:     hash['authors']     = authors
47:     hash['title']       = title
48:     hash['journal']     = journal
49:     hash['volume']      = volume
50:     hash['issue']       = issue
51:     hash['pages']       = pages
52:     hash['year']        = year
53:     hash['pubmed']      = pmid
54:     hash['medline']     = ui
55:     hash['abstract']    = abstract
56:     hash['mesh']        = mesh
57:     hash['affiliations'] = affiliations
58: 
59:     hash.delete_if { |k, v| v.nil? or v.empty? }
60: 
61:     return Reference.new(hash)
62:   end

so()

SO - Source

  Composite field containing bibliographic information.

[Source]

     # File lib/bio/db/medline.rb, line 173
173:   def so
174:     @pubmed['SO'].strip
175:   end

source()

Alias for so

ta()

TA - Journal Title Abbreviation

  Standard journal title abbreviation.

[Source]

    # File lib/bio/db/medline.rb, line 82
82:   def ta
83:     @pubmed['TA'].gsub(/\s+/, ' ').strip
84:   end

ti()

TI - Title Words

  The title of the article.

[Source]

     # File lib/bio/db/medline.rb, line 133
133:   def ti
134:     @pubmed['TI'].gsub(/\s+/, ' ').strip
135:   end

title()

Alias for ti

ui()

UI - MEDLINE Unique Identifier

  Unique number assigned to each MEDLINE citation.

[Source]

    # File lib/bio/db/medline.rb, line 76
76:   def ui
77:     @pubmed['UI'].strip
78:   end

vi()

VI - Volume

  Journal volume.

[Source]

    # File lib/bio/db/medline.rb, line 89
89:   def vi
90:     @pubmed['VI'].strip
91:   end

volume()

Alias for vi

year()

[Source]

     # File lib/bio/db/medline.rb, line 127
127:   def year
128:     dp[0,4]
129:   end

Description

Examples

Methods

Attributes

Public Class methods

Public Instance methods