Class | Bio::PubMed |
In: |
lib/bio/io/pubmed.rb
|
Parent: | Bio::NCBI::REST |
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:
http://www.ncbi.nlm.nih.gov/entrez/query/static/overview.html
http://www.ncbi.nlm.nih.gov/entrez/query/static/help/pmhelp.html
http://www.ncbi.nlm.nih.gov/entrez/utils/utils_index.html
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helplinks.chapter.linkshelp
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)
# File lib/bio/io/pubmed.rb, line 204 204: def self.efetch(*args) 205: self.new.efetch(*args) 206: end
# File lib/bio/io/pubmed.rb, line 200 200: def self.esearch(*args) 201: self.new.esearch(*args) 202: end
# File lib/bio/io/pubmed.rb, line 216 216: def self.pmfetch(*args) 217: self.new.pmfetch(*args) 218: end
# File lib/bio/io/pubmed.rb, line 212 212: def self.query(*args) 213: self.new.query(*args) 214: end
# File lib/bio/io/pubmed.rb, line 208 208: def self.search(*args) 209: self.new.search(*args) 210: end
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:
Returns: | Array of MEDLINE formatted String |
# File lib/bio/io/pubmed.rb, line 117 117: def efetch(ids, hash = {}) 118: opts = { "db" => "pubmed", "rettype" => "medline" } 119: opts.update(hash) 120: result = super(ids, opts) 121: if !opts["retmode"] or opts["retmode"] == "text" 122: result = result.split(/\n\n+/) 123: end 124: result 125: end
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:
Returns: | array of PubMed IDs or a number of results |
# 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
Retrieve PubMed entry by PMID and returns MEDLINE formatted string using entrez pmfetch.
Arguments:
Returns: | MEDLINE formatted String |
# File lib/bio/io/pubmed.rb, line 183 183: def pmfetch(id) 184: host = "www.ncbi.nlm.nih.gov" 185: path = "/entrez/utils/pmfetch.fcgi?tool=bioruby&mode=text&report=medline&db=PubMed&id=" 186: 187: ncbi_access_wait 188: 189: http = Bio::Command.new_http(host) 190: response = http.get(path + CGI.escape(id.to_s)) 191: result = response.body 192: if result =~ /#{id}\s+Error/ 193: raise( result ) 194: else 195: result = result.gsub("\r", "\n").squeeze("\n").gsub(/<\/?pre>/, '') 196: return result 197: end 198: end
Retrieve PubMed entry by PMID and returns MEDLINE formatted string using entrez query.
Arguments:
Returns: | MEDLINE formatted String |
# File lib/bio/io/pubmed.rb, line 153 153: def query(*ids) 154: host = "www.ncbi.nlm.nih.gov" 155: path = "/sites/entrez?tool=bioruby&cmd=Text&dopt=MEDLINE&db=PubMed&uid=" 156: list = ids.collect { |x| CGI.escape(x.to_s) }.join(",") 157: 158: ncbi_access_wait 159: 160: http = Bio::Command.new_http(host) 161: response = http.get(path + list) 162: result = response.body 163: result = result.scan(/<pre>\s*(.*?)<\/pre>/m).flatten 164: 165: if result =~ /id:.*Error occurred/ 166: # id: xxxxx Error occurred: Article does not exist 167: raise( result ) 168: else 169: if ids.size > 1 170: return result 171: else 172: return result.first 173: end 174: end 175: end
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:
Returns: | array of PubMed IDs |
# File lib/bio/io/pubmed.rb, line 134 134: def search(str) 135: host = "www.ncbi.nlm.nih.gov" 136: path = "/sites/entrez?tool=bioruby&cmd=Search&doptcmdl=Brief&db=PubMed&term=" 137: 138: ncbi_access_wait 139: 140: http = Bio::Command.new_http(host) 141: response = http.get(path + CGI.escape(str)) 142: result = response.body 143: result = result.scan(/value="(\d+)" id="UidCheckBox"/m).flatten 144: return result 145: end