NCBIDB
NCBI PubMed/MEDLINE database class.
medline = Bio::MEDLINE.new(txt) medline.reference medline.pmid == medline.entry_id medilne.mesh
# 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
AB - Abstract
Abstract.
# File lib/bio/db/medline.rb, line 145 def ab @pubmed['AB'].gsub(/\s+/, ' ').strip end
AD - Affiliation
Institutional affiliation and address of the first author, and grant numbers.
# File lib/bio/db/medline.rb, line 193 def ad @pubmed['AD'].strip.split(/\n/) end
AU - Author Name
Authors' names.
# File lib/bio/db/medline.rb, line 152 def au @pubmed['AU'].strip end
AID - Article Identifier
Article ID values may include the pii (controlled publisher identifier) or doi (Digital Object Identifier).
# File lib/bio/db/medline.rb, line 201 def doi @pubmed['AID'][/(\S+) \[doi\]/, 1] end
DP - Publication Date
The date the article was published.
# File lib/bio/db/medline.rb, line 127 def dp @pubmed['DP'].strip end
IP - Issue
The number of the issue, part, or supplement of the journal in which the article was published.
# File lib/bio/db/medline.rb, line 102 def ip @pubmed['IP'].strip end
MH - MeSH Terms
NLM's controlled vocabulary.
# File lib/bio/db/medline.rb, line 185 def mh @pubmed['MH'].strip.split(/\n/) end
# 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 - Page Number
The full pagination of the article.
# File lib/bio/db/medline.rb, line 109 def pg @pubmed['PG'].strip end
# File lib/bio/db/medline.rb, line 205 def pii @pubmed['AID'][/(\S+) \[pii\]/, 1] end
PMID - PubMed Unique Identifier
Unique number assigned to each PubMed citation.
# File lib/bio/db/medline.rb, line 74 def pmid @pubmed['PMID'].strip end
PT - Publication Type
The type of material the article represents.
# File lib/bio/db/medline.rb, line 278 def pt @pubmed['PT'].strip.split(/\n/) end
returns a Reference object.
# 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 - Source
Composite field containing bibliographic information.
# File lib/bio/db/medline.rb, line 178 def so @pubmed['SO'].strip end
TA - Journal Title Abbreviation
Standard journal title abbreviation.
# File lib/bio/db/medline.rb, line 87 def ta @pubmed['TA'].gsub(/\s+/, ' ').strip end
TI - Title Words
The title of the article.
# File lib/bio/db/medline.rb, line 138 def ti @pubmed['TI'].gsub(/\s+/, ' ').strip end
UI - MEDLINE Unique Identifier
Unique number assigned to each MEDLINE citation.
# File lib/bio/db/medline.rb, line 81 def ui @pubmed['UI'].strip end
VI - Volume
Journal volume.
# File lib/bio/db/medline.rb, line 94 def vi @pubmed['VI'].strip end
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