Class Bio::PubMed
In: lib/bio/io/pubmed.rb
Parent: Bio::NCBI::REST

Description

The Bio::PubMed class provides several ways to retrieve bibliographic information from the PubMed database at 

  http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed

Basically, two types of queries are possible:

The different methods within the same group are interchangeable and should return the same result.

Additional information about the MEDLINE format and PubMed programmable APIs can be found on the following websites:

  • PubMed Overview: 
      http://www.ncbi.nlm.nih.gov/entrez/query/static/overview.html
  • PubMed help: 
      http://www.ncbi.nlm.nih.gov/entrez/query/static/help/pmhelp.html
  • Entrez utilities index: 
       http://www.ncbi.nlm.nih.gov/entrez/utils/utils_index.html
  • How to link: 
      http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helplinks.chapter.linkshelp

Usage

  require 'bio'

  # If you don't know the pubmed ID:
  Bio::PubMed.esearch("(genome AND analysis) OR bioinformatics").each do |x|
    p x
  end

  Bio::PubMed.search("(genome AND analysis) OR bioinformatics").each do |x|
    p x
  end

  # To retrieve the MEDLINE entry for a given PubMed ID:
  puts Bio::PubMed.efetch("10592173", "14693808")
  puts Bio::PubMed.query("10592173")
  puts Bio::PubMed.pmfetch("10592173")

  # This can be converted into a Bio::MEDLINE object:
  manuscript = Bio::PubMed.query("10592173")
  medline = Bio::MEDLINE.new(manuscript)

Methods

efetch   efetch   esearch   esearch   pmfetch   pmfetch   query   query   search   search  

Public Class methods

efetch(*args)

[Source]

     # File lib/bio/io/pubmed.rb, line 200
200:   def self.efetch(*args)
201:     self.new.efetch(*args)
202:   end
esearch(*args)

[Source]

     # File lib/bio/io/pubmed.rb, line 196
196:   def self.esearch(*args)
197:     self.new.esearch(*args)
198:   end
pmfetch(*args)

[Source]

     # File lib/bio/io/pubmed.rb, line 212
212:   def self.pmfetch(*args)
213:     self.new.pmfetch(*args)
214:   end
query(*args)

[Source]

     # File lib/bio/io/pubmed.rb, line 208
208:   def self.query(*args)
209:     self.new.query(*args)
210:   end
search(*args)

[Source]

     # File lib/bio/io/pubmed.rb, line 204
204:   def self.search(*args)
205:     self.new.search(*args)
206:   end

Public Instance methods

efetch(ids, hash = {})

Retrieve PubMed entry by PMID and returns MEDLINE formatted string using entrez efetch. Multiple PubMed IDs can be provided: 

  Bio::PubMed.efetch(123)
  Bio::PubMed.efetch([123,456,789])

Arguments:

  • ids: list of PubMed IDs (required)
  • hash: hash of E-Utils options
    • retmode: "xml", "html", …
    • rettype: "medline", …
    • retmax: integer (default 100)
    • retstart: integer
    • field
    • reldate
    • mindate
    • maxdate
    • datetype
Returns:Array of MEDLINE formatted String

[Source]

     # File lib/bio/io/pubmed.rb, line 117
117:   def efetch(ids, hash = {})
118:     opts = { "db" => "pubmed", "rettype"  => "medline" }
119:     opts.update(hash)
120:     super(ids, opts)
121:   end
esearch(str, hash = {})

Search the PubMed database by given keywords using E-Utils and returns an array of PubMed IDs.

For information on the possible arguments, see eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html#PubMed

Arguments:

  • str: query string (required)
  • hash: hash of E-Utils options
    • retmode: "xml", "html", …
    • rettype: "medline", …
    • retmax: integer (default 100)
    • retstart: integer
    • field
    • reldate
    • mindate
    • maxdate
    • datetype
Returns:array of PubMed IDs or a number of results

[Source]

    # File lib/bio/io/pubmed.rb, line 93
93:   def esearch(str, hash = {})
94:     opts = { "db" => "pubmed" }
95:     opts.update(hash)
96:     super(str, opts)
97:   end
pmfetch(id)

Retrieve PubMed entry by PMID and returns MEDLINE formatted string using entrez pmfetch.

Arguments:

Returns:MEDLINE formatted String

[Source]

     # File lib/bio/io/pubmed.rb, line 179
179:   def pmfetch(id)
180:     host = "www.ncbi.nlm.nih.gov"
181:     path = "/entrez/utils/pmfetch.fcgi?tool=bioruby&mode=text&report=medline&db=PubMed&id="
182: 
183:     ncbi_access_wait
184: 
185:     http = Bio::Command.new_http(host)
186:     response = http.get(path + CGI.escape(id.to_s))
187:     result = response.body
188:     if result =~ /#{id}\s+Error/
189:       raise( result )
190:     else
191:       result = result.gsub("\r", "\n").squeeze("\n").gsub(/<\/?pre>/, '')
192:       return result
193:     end
194:   end
query(*ids)

Retrieve PubMed entry by PMID and returns MEDLINE formatted string using entrez query.

Arguments:

Returns:MEDLINE formatted String

[Source]

     # File lib/bio/io/pubmed.rb, line 149
149:   def query(*ids)
150:     host = "www.ncbi.nlm.nih.gov"
151:     path = "/sites/entrez?tool=bioruby&cmd=Text&dopt=MEDLINE&db=PubMed&uid="
152:     list = ids.collect { |x| CGI.escape(x.to_s) }.join(",")
153: 
154:     ncbi_access_wait
155: 
156:     http = Bio::Command.new_http(host)
157:     response = http.get(path + list)
158:     result = response.body
159:     result = result.scan(/<pre>\s*(.*?)<\/pre>/m).flatten
160: 
161:     if result =~ /id:.*Error occurred/
162:       # id: xxxxx Error occurred: Article does not exist
163:       raise( result )
164:     else
165:       if ids.size > 1
166:         return result
167:       else
168:         return result.first
169:       end
170:     end
171:   end
search(str)

Search the PubMed database by given keywords using entrez query and returns an array of PubMed IDs. Caution: this method returns the first 20 hits only. Instead, use of the ‘esearch’ method is strongly recomended.

Arguments:

  • id: query string (required)
Returns:array of PubMed IDs

[Source]

     # File lib/bio/io/pubmed.rb, line 130
130:   def search(str)
131:     host = "www.ncbi.nlm.nih.gov"
132:     path = "/sites/entrez?tool=bioruby&cmd=Search&doptcmdl=Brief&db=PubMed&term="
133: 
134:     ncbi_access_wait
135: 
136:     http = Bio::Command.new_http(host)
137:     response = http.get(path + CGI.escape(str))
138:     result = response.body
139:     result = result.scan(/value="(\d+)" id="UidCheckBox"/m).flatten
140:     return result
141:   end

[Validate]