rbbt 1.0.0

data/install_scripts/organisms/human.Rakefile

@@ -0,0 +1,145 @@
+require __FILE__.sub(/[^\/]*$/,'') + '../rake-include'
+
+$name = "Homo sapiens"
+
+
+$native_id = "Entrez Gene ID"
+
+$entrez2native = {
+  :tax => 9606,
+  :fix => nil,
+  :check => proc{|code| false},
+}
+
+$lexicon = {
+  :biomart => {
+    :database => 'hsapiens_gene_ensembl',
+    :main => ['Entrez Gene ID' , "entrezgene"], 
+    :extra => [ 
+      [ 'Associated Gene Name' , "external_gene_id"], 
+      [ 'HGNC symbol', "hgnc_symbol"  ],
+      [ 'HGNC automatic gene name', "hgnc_automatic_gene_name"  ],
+      [ 'HGNC curated gene name ', "hgnc_curated_gene_name"  ],
+    ],
+  }
+
+}
+
+$identifiers = {
+  :biomart => {
+    :database => 'hsapiens_gene_ensembl',
+    :main => ['Entrez Gene ID' , "entrezgene"], 
+    :extra => [ 
+      [ 'Ensembl Gene ID', "ensembl_gene_id"  ],
+      [ 'Ensembl Protein ID', "ensembl_peptide_id"  ],
+      [ 'Associated Gene Name', "external_gene_id"  ],
+      [ 'CCDS ID', "ccds"  ],
+      [ 'Protein ID', "protein_id"  ],
+      [ 'RefSeq Protein ID', "refseq_peptide"  ],
+      [ 'Unigene ID', "unigene"  ],
+      [ 'UniProt/SwissProt ID', "uniprot_swissprot"  ],
+      [ 'UniProt/SwissProt Accession', "uniprot_swissprot_accession"  ],
+      [ 'HGNC ID', "hgnc_id", 'HGNC'],
+      ['EMBL (Genbank) ID' , "embl"] , 
+
+      # Affymetrix
+      [ 'AFFY HC G110', 'affy_hc_g110' ],
+      [ 'AFFY HG FOCUS', 'affy_hg_focus' ],
+      [ 'AFFY HG U133-PLUS-2', 'affy_hg_u133_plus_2' ],
+      [ 'AFFY HG U133A_2', 'affy_hg_u133a_2' ],
+      [ 'AFFY HG U133A', 'affy_hg_u133a' ],
+      [ 'AFFY HG U133B', 'affy_hg_u133b' ],
+      [ 'AFFY HG U95AV2', 'affy_hg_u95av2' ],
+      [ 'AFFY HG U95B', 'affy_hg_u95b' ],
+      [ 'AFFY HG U95C', 'affy_hg_u95c' ],
+      [ 'AFFY HG U95D', 'affy_hg_u95d' ],
+      [ 'AFFY HG U95E', 'affy_hg_u95e' ],
+      [ 'AFFY HG U95A', 'affy_hg_u95a' ],
+      [ 'AFFY HUGENEFL', 'affy_hugenefl' ],
+      [ 'AFFY HuEx', 'affy_huex_1_0_st_v2' ],
+      [ 'AFFY HuGene', 'affy_hugene_1_0_st_v1' ],
+      [ 'AFFY U133 X3P', 'affy_u133_x3p' ],
+      [ 'Agilent WholeGenome',"agilent_wholegenome" ],
+      [ 'Agilent CGH 44b', 'agilent_cgh_44b' ],
+      [ 'Codelink ID', 'codelink' ],
+      [ 'Illumina HumanWG 6 v2', 'illumina_humanwg_6_v2' ],
+      [ 'Illumina HumanWG 6 v3', 'illumina_humanwg_6_v3' ],
+
+    ],
+    :filter => [],
+  }
+}
+
+$go = {
+ :url => "http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/gene-associations/gene_association.goa_human.gz?rev=HEAD",
+ :code => 2,
+ :go   => 4,
+ :pmid => 5,
+}
+
+$query = '"humans"[MeSH Terms] AND ((("genes"[TIAB] NOT Medline[SB]) OR "genes"[MeSH Terms] OR gene[Text Word]) OR (("proteins"[TIAB] NOT Medline[SB]) OR "proteins"[MeSH Terms] OR protein[Text Word])) AND (hasabstract[text] AND "humans"[MeSH Terms] AND English[lang])'
+##########################
+
+require 'rbbt/util/index'
+
+Rake::Task['gene.go'].clear
+file 'gene.go' => ['identifiers'] do 
+  if File.exists? 'identifiers'
+    require 'rbbt/sources/organism'
+    index = Organism.id_index('human', :other => ['Associated Gene Name'])
+    data = Open.to_hash($go[:url], :native => $go[:code], :extra => $go[:go], :exclude => $go[:exclude])
+
+    data = data.collect{|code, value_lists|
+      code = index[code]
+      [code, value_lists.flatten.select{|ref| ref =~ /GO:\d+/}.collect{|ref| ref.match(/(GO:\d+)/)[1]}]
+    }.select{|p| p[0] && p[1].any?}
+
+    Open.write('gene.go', 
+               data.collect{|p| 
+                 p[1].uniq.collect{|go|
+                   "#{p[0]}\t#{go}"
+                 }.join("\n")
+               }.join("\n")
+              )
+  end
+end
+
+Rake::Task['gene_go.pmid'].clear
+file 'gene_go.pmid' => ['identifiers'] do
+  if File.exists? 'identifiers'
+    index = Index.index('identifiers')
+    data = Open.to_hash($go[:url], :native => $go[:code], :extra => $go[:pmid], :exclude => $go[:exclude])
+
+    data = data.collect{|code, value_lists|
+      code = index[code]
+      [code, value_lists.flatten.select{|ref| ref =~ /PMID:\d+/}.collect{|ref| ref.match(/PMID:(\d+)/)[1]}]
+    }.select{|p| p[0] && p[1].any?}
+
+    Open.write('gene_go.pmid', 
+               data.collect{|p| 
+                 p[1].uniq.collect{|pmid|
+                   "#{p[0]}\t#{pmid}"
+                 }.join("\n")
+               }.join("\n")
+              )
+  end
+end
+
+
+Rake::Task['lexicon'].clear
+file 'lexicon' => ['identifiers'] do
+  if File.exists? 'identifiers'
+    require 'rbbt/sources/organism'
+    HGNC_URL = 'http://www.genenames.org/cgi-bin/hgnc_downloads.cgi?title=HGNC+output+data&hgnc_dbtag=on&col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_prev_sym&col=gd_prev_name&col=gd_aliases&col=gd_name_aliases&col=gd_pub_acc_ids&status=Approved&status_opt=2&level=pri&=on&where=&order_by=gd_app_sym_sort&limit=&format=text&submit=submit&.cgifields=&.cgifields=level&.cgifields=chr&.cgifields=status&.cgifields=hgnc_dbtag'
+    names = Open.to_hash(HGNC_URL, :exclude => proc{|l| l.match(/^HGNC ID/)}, :flatten => true)
+    translations = Organism.id_index('human', :native => 'Entrez Gene ID', :other => ['HGNC ID'])
+
+    Open.write('lexicon',
+               names.collect{|code, names|
+                 next unless translations[code]
+                 ([translations[code]] + names).join("\t")
+               }.compact.join("\n")
+               )
+  end
+
+end

data/install_scripts/organisms/mgi.Rakefile

@@ -0,0 +1,77 @@
+require __FILE__.sub(/[^\/]*$/,'') + '../rake-include'
+
+$name = "Mus musculus"
+
+
+$native_id = "MGI DB ID"
+
+$entrez2native = {
+  :tax => 10090,
+  :fix => nil,
+  :check => proc{|code| code.match(/^MGI/)},
+}
+
+$lexicon = {
+  :file => {
+    :url =>  "ftp://ftp.informatics.jax.org/pub/reports/MGI_Coordinate.rpt",
+    :native => 0,
+    :extra => [2,3],
+    :exclude => proc{|l| l.split(/\t/)[1] != "Gene"},
+  },
+}
+
+$identifiers = {
+  :file => {
+    :url =>  "ftp://ftp.informatics.jax.org/pub/reports/MGI_Coordinate.rpt",
+    :native => 0,
+    :extra => [],
+    :exclude => proc{|l| l.split(/\t/)[1] != "Gene"},
+  },
+  :biomart => {
+    :database => 'mmusculus_gene_ensembl',
+    :main => ['MGI DB ID', 'mgi_id'] , 
+    :extra => [ 
+      ['Associated Gene Name' , "external_gene_id"], 
+      ['Protein ID' , "protein_id"] , 
+      ['UniProt/SwissProt ID' , "uniprot_swissprot"] , 
+      ['Unigene ID' , "unigene"] , 
+      ['UniProt/SwissProt Accession' , "uniprot_swissprot_accession"] , 
+      ['RefSeq Protein ID' , "refseq_peptide"] , 
+      ['EMBL (Genbank) ID' , "embl"] , 
+
+      ['Affy mg u74a',"affy_mg_u74a" ],
+      ['Affy mg u74av2',"affy_mg_u74av2" ],
+      ['Affy mg u74b',"affy_mg_u74b" ],
+      ['Affy mg u74bv2',"affy_mg_u74bv2" ],
+      ['Affy mg u74c',"affy_mg_u74c" ],
+      ['Affy mg u74cv2',"affy_mg_u74cv2" ],
+      ['Affy moe430a',"affy_moe430a" ],
+      ['Affy moe430b',"affy_moe430b" ],
+      ['AFFY MoEx',"affy_moex_1_0_st_v1" ],
+      ['AFFY MoGene',"affy_mogene_1_0_st_v1" ],
+      ['Affy mouse430 2',"affy_mouse430_2" ],
+      ['Affy mouse430a 2',"affy_mouse430a_2" ],
+      ['Affy mu11ksuba',"affy_mu11ksuba" ],
+      ['Affy mu11ksubb',"affy_mu11ksubb" ],
+      ['Agilent WholeGenome',"agilent_wholegenome" ],
+      ['Codelink ID',"codelink" ],
+      ['Illumina MouseWG 6 v1',"illumina_mousewg_6_v1" ],
+      ['Illumina MouseWG 6 v2',"illumina_mousewg_6_v2" ],
+
+    ],
+    :filter => ['with_mgi'], # This is needed as the filter is not with_mgi_id as was expected
+  }
+}
+
+$go = {
+  :url => "ftp://ftp.geneontology.org/go/gene-associations/gene_association.mgi.gz",
+  :code => 1,
+  :go   => 4,
+  :pmid => 5,
+}
+
+$query = '(("mice"[TIAB] NOT Medline[SB]) OR "mice"[MeSH Terms] OR mouse[Text Word]) AND ((("genes"[TIAB] NOT Medline[SB]) OR "genes"[MeSH Terms] OR gene[Text Word]) OR (("proteins"[TIAB] NOT Medline[SB]) OR "proteins"[MeSH Terms] OR protein[Text Word]))'
+##########################
+
+
+

data/install_scripts/organisms/pombe.Rakefile

@@ -0,0 +1,40 @@
+require __FILE__.sub(/[^\/]*$/,'') + '../rake-include'
+
+$name = "Schizosaccharomyces pombe"
+
+
+$native_id = "GeneDB Id"
+
+$entrez2native = {
+  :tax => 4896,
+  :fix => proc{|code| code.sub(/GeneDB:SP/,'SP') },
+  :check => proc{|code| code.match(/^SP/)},
+}
+
+$lexicon = {
+  :file => {
+    :url => 'ftp://ftp.sanger.ac.uk/pub/yeast/pombe/Mappings/allNames.txt',
+    :native => 0,
+    :extra => [1,2,3,4,5,6,7,8]
+  },
+}
+
+$identifiers = {
+  :file => {
+    :url => 'ftp://ftp.sanger.ac.uk/pub/yeast/pombe/Mappings/allNames.txt',
+    :native => 0,
+    :extra => [],
+  },
+}
+
+$go = {
+  :url => "ftp://ftp.sanger.ac.uk/pub/yeast/pombe/Gene_ontology/gene_association.GeneDB_Spombe",
+  :code => 1,
+  :go   => 4,
+  :pmid => 5,
+}
+
+$query = 'pombe[All Fields] AND (hasabstract[text] AND English[lang])'
+####
+
+

data/install_scripts/organisms/rake-include.rb

@@ -0,0 +1,258 @@
+require 'rbbt'
+require 'rbbt/util/open'
+require 'rbbt/util/arrayHash'
+require 'rbbt/sources/biomart'
+require 'rbbt/sources/entrez'
+require 'rbbt/sources/pubmed'
+
+
+
+file 'name' do
+  Open.write('name', $name)
+end
+
+file 'all.pmid' do
+  Open.write('all.pmid', PubMed.query($query).join("\n"))
+end
+
+file 'lexicon' do
+  begin
+
+    data = nil
+    # Read from file
+    if $lexicon[:file]
+      file = Open.to_hash($lexicon[:file][:url], $lexicon[:file])
+      data = ArrayHash.new(file, $native_id)
+    end
+
+    # Translate from entrez to native if needed
+    if $entrez2native
+      translations = {}
+      Entrez.entrez2native(*$entrez2native.values_at(:tax,:native,:fix,:check)).
+        each{|k,v|
+          translations[k] = [v.join("|")]
+      }
+      translations_data = ArrayHash.new(translations,'Entrez Gene ID', [$native_id])
+      if data
+        data.merge(translations_data)
+      else
+        data = translations_data
+      end
+
+    end
+
+
+    # Read from Biomart and merge with previous data
+    if $lexicon[:biomart]
+      biomart = {}
+      
+      BioMart.query(
+        $lexicon[:biomart][:database],
+        $lexicon[:biomart][:main][1],
+        $lexicon[:biomart][:extra].collect{|v| v[1]},
+        $lexicon[:biomart][:filter]
+      ).each{|key, values_list|
+        values = values_list.values_at(*$lexicon[:biomart][:extra].collect{|v| v[1]}).compact.collect{|list| list.select{|e| e.to_s != ""}.uniq.join("|")}
+        biomart[key] = values
+      }
+
+      biomart_data = ArrayHash.new(biomart, $lexicon[:biomart][:main][0], $lexicon[:biomart][:extra].collect{|v| v[0]})
+
+      if data
+        if $lexicon[:biomart][:extra].collect{|v| v[1]}.include?( $native_id )|| $lexicon[:biomart][:main][0] == $native_id
+          field = $native_id 
+        else
+          field =  'Entrez Gene ID'
+        end
+        data.merge(biomart_data, field)
+      else
+        data = biomart_data
+      end
+    end
+
+    if $entrez2native
+      gene_alias = {}
+      Entrez.entrez2native($entrez2native[:tax],4).
+        each{|k,v|
+        gene_alias[k] = [v.select{|e| e.to_s != ""}.join("|")]
+      }
+      if gene_alias.keys.any?
+        gene_alias_data = ArrayHash.new(gene_alias,'Entrez Gene ID', ['Entrez Gene Alias'])
+        data.merge(gene_alias_data, 'Entrez Gene ID')
+      end
+    end
+
+    data.remove('Entrez Gene ID')
+    data.clean
+    Open.write('lexicon', data.data.collect{|code, name_lists|
+      "#{ code }\t" + name_lists.flatten.select{|n| n.to_s != ""}.uniq.join("\t")
+    }.join("\n"))
+
+rescue Entrez::NoFile
+  puts "Lexicon not produced for #{$name}, install the entrez gene_info file (rbbt_config install entrez)."
+end
+end
+
+
+file 'identifiers' do
+
+  begin
+    data = nil
+    if $identifiers[:file]
+      file = Open.to_hash($identifiers[:file][:url], $identifiers[:file])
+      data = ArrayHash.new(file, $native_id, $identifiers[:file][:fields])
+    end
+
+    # Translate from entrez to native if needed
+    if $entrez2native
+      translations = {}
+      Entrez.entrez2native(*$entrez2native.values_at(:tax,:native,:fix,:check)).
+        each{|k,v|
+          translations[k] = [v.join("|")]
+      }
+      if translations.keys.any?
+        translations_data = ArrayHash.new(translations,'Entrez Gene ID', [$native_id])
+        if data
+          data.merge(translations_data)
+        else
+          data = translations_data
+        end
+      end
+
+    end
+
+
+    # Read from Biomart and merge with previous data
+    if $identifiers[:biomart]
+      biomart = {}
+      
+      BioMart.query(
+        $identifiers[:biomart][:database],
+        $identifiers[:biomart][:main][1],
+        $identifiers[:biomart][:extra].collect{|v| v[1]},
+        $identifiers[:biomart][:filter]
+      ).each{|key, values_list|
+        values = values_list.values_at(*$identifiers[:biomart][:extra].collect{|v| v[1]}).compact.collect{|list| list.select{|e| e.to_s != ""}.uniq.join("|")}
+        biomart[key] = values
+      }
+
+      biomart_data = ArrayHash.new(biomart, $identifiers[:biomart][:main][0], $identifiers[:biomart][:extra].collect{|v| v[0]})
+      $identifiers[:biomart][:extra].each{|values|
+        if values[2]
+          biomart_data.process(values[0]){|n| "#{values[2]}:#{n}"}
+        end
+      }
+
+
+      if data
+        if $identifiers[:biomart][:extra].collect{|v| v[1]}.include?( $native_id ) || $identifiers[:biomart][:main][0] == $native_id
+          field = $native_id 
+        else
+          field = 'Entrez Gene ID'
+        end
+        data.merge(biomart_data, field)
+      else
+        data = biomart_data
+      end
+    end
+
+
+    # Add the alias at the end
+    if $entrez2native
+      gene_alias = {}
+      Entrez.entrez2native($entrez2native[:tax],4).
+       each{|k,v|
+         gene_alias[k] = [v.join("|")]
+      }
+      if gene_alias.keys.any?
+        gene_alias_data = ArrayHash.new(gene_alias,'Entrez Gene ID', ['Entrez Gene Alias'])
+        if data
+          data.merge(gene_alias_data, 'Entrez Gene ID')
+        else
+          data = gene_alias_data
+        end
+      end
+    end
+
+
+
+    # Write ids to file
+    fout = File.open('identifiers', 'w')
+    fout.puts "##{$native_id}\t" + data.fields.join("\t")
+    data.clean
+    data.data.each{|code, values|
+      fout.puts code + "\t" + values.join("\t")
+    }
+    fout.close
+
+  rescue Entrez::NoFile
+    puts "Identifiers not produced for #{$name}, install the entrez gene_info file (rbbt_config install entrez)."
+  end
+end
+
+
+file 'gene.go' do
+  data = Open.to_hash($go[:url], :native => $go[:code], :extra => $go[:go], :exclude => $go[:exclude], :fix => $go[:fix])
+
+  data = data.collect{|code, value_lists|
+    [code, value_lists.flatten.select{|ref| ref =~ /GO:\d+/}.collect{|ref| ref.match(/(GO:\d+)/)[1]}]
+  }.select{|p|  p[1].any?}
+
+  Open.write('gene.go', 
+              data.collect{|p| 
+                p[1].uniq.collect{|go|
+                  "#{p[0]}\t#{go}"
+                }.join("\n")
+              }.join("\n")
+            )
+end
+
+file 'gene_go.pmid' do
+  data = Open.to_hash($go[:url], :native => $go[:code], :extra => $go[:pmid], :exclude => $go[:exclude], :fix => $go[:fix])
+
+  data = data.collect{|code, value_lists|
+    [code, value_lists.flatten.select{|ref| ref =~ /PMID:\d+/}.collect{|ref| ref.match(/PMID:(\d+)/)[1]}]
+  }.select{|p|  p[1].any?}
+
+  Open.write('gene_go.pmid', 
+              data.collect{|p| 
+                p[1].uniq.collect{|pmid| "#{p[0]}\t#{pmid}" }.join("\n")
+              }.join("\n")
+            )
+end
+
+
+file 'gene.pmid' do
+  begin
+    translations = Entrez.entrez2native(*$entrez2native.values_at(:tax,:native,:fix,:check)) if $native_id != "Entrez Gene ID"
+
+    data = Entrez.entrez2pubmed($entrez2native[:tax])
+
+    Open.write('gene.pmid',
+               data.collect{|code,pmids|
+      next if translations && ! translations[code]
+      code = translations[code].first if translations 
+      pmids.collect{|pmid|
+                 "#{ code }\t#{pmid}"
+      }.compact.join("\n")
+    }.compact.join("\n")
+              )
+  rescue Entrez::NoFile
+    puts "Gene article associations from entrez not produced, install the gene2pumbed file (rbbt_config install entrez)."
+  end
+
+end
+
+
+
+
+task 'all' => ['name', 'lexicon', 'identifiers', 'gene_go.pmid', 'gene.pmid', 'gene.go', 'all.pmid']
+task 'clean' do
+  `rm -f 'name' 'lexicon' 'identifiers' 'gene_go.pmid' 'gene.pmid' 'gene.go' 'all.pmid'`
+end
+
+task 'update' do
+  Rake::Task['clean'].invoke if $force
+  Rake::Task['all'].invoke
+end
+

data/install_scripts/organisms/rgd.Rakefile

@@ -0,0 +1,88 @@
+require __FILE__.sub(/[^\/]*$/,'') + '../rake-include'
+
+$name = "Rattus norvegicus"
+
+
+$native_id = "RGD DB ID"
+
+$entrez2native = {
+  :tax => 10116,
+  :check => proc{|code| code.match(/^RGD/)},
+}
+
+$lexicon = {
+  :file => {
+    :url => "ftp://rgd.mcw.edu/pub/data_release/gene_association.rgd.gz",
+    :native => 1,
+    :extra => [2,9],
+    :exclude => proc{|l| !l.match(/^RGD/)}
+  },
+}
+
+$identifiers = {
+  :file => {
+    :url => "ftp://rgd.mcw.edu/pub/data_release/gene_association.rgd.gz",
+    :native => 1,
+    :extra => [],
+    :exclude => proc{|l| !l.match(/^RGD/)}
+  },
+  :biomart => {
+    :database => 'rnorvegicus_gene_ensembl',
+    :main =>  ['Entrez Gene ID' , "entrezgene"], 
+    :extra => [ 
+      ['Associated Gene Name' , "external_gene_id"], 
+      ['Protein ID' , "protein_id"] , 
+      ['UniProt/SwissProt ID' , "uniprot_swissprot"] , 
+      ['UniProt/SwissProt Accession' , "uniprot_swissprot_accession"] , 
+      ['RefSeq Protein ID' , "refseq_peptide"] , 
+      ['EMBL (Genbank) ID' , "embl"] , 
+
+      ['Affy rae230a', "affy_rae230a"],
+      ['Affy rae230b', "affy_rae230b"],
+      ['Affy RaGene', "affy_ragene_1_0_st_v1"],
+      ['Affy rat230 2', "affy_rat230_2"],
+      ['Affy RaEx', "affy_raex_1_0_st_v1"],
+      ['Affy rg u34a', "affy_rg_u34a"],
+      ['Affy rg u34b', "affy_rg_u34b"],
+      ['Affy rg u34c', "affy_rg_u34c"],
+      ['Affy rn u34', "affy_rn_u34"],
+      ['Affy rt u34', "affy_rt_u34"],
+      ['Agilent WholeGenome',"agilent_wholegenome" ],
+      ['Codelink ID ', "codelink"],
+
+
+    ],
+    :filter => [],
+  }
+}
+
+$go = {
+  :url => "ftp://rgd.mcw.edu/pub/data_release/gene_association.rgd.gz",
+  :exclude => proc{|l| !l.match(/^RGD/)},
+  :code => 1,
+  :go   => 4,
+  :pmid => 5,
+}
+
+$query = '(("mice"[TIAB] NOT Medline[SB]) OR "mice"[MeSH Terms] OR mouse[Text Word]) AND ((("proteins"[TIAB] NOT Medline[SB]) OR "proteins"[MeSH Terms] OR protein[Text Word]) OR (("genes"[TIAB] NOT Medline[SB]) OR "genes"[MeSH Terms] OR gene[Text Word]))  AND hasabstract[text] AND English[lang]'
+
+#{{{ Redefines
+
+module Open
+
+  class << self
+    alias_method :old_read, :read
+
+    def read(url, options = {})
+      data = old_read(url, options)
+
+      if url =~ /gene_association.rgd.gz/
+        return data.collect{|l| l.gsub(/^RGD\t/,"RGD\tRGD:")}.join("\n")
+      else
+        return data
+      end
+
+    end
+  end
+end
+

data/install_scripts/organisms/sgd.Rakefile

@@ -0,0 +1,66 @@
+require __FILE__.sub(/[^\/]*$/,'') + '../rake-include'
+
+$name = "Saccharomyces cerevisiae"
+
+
+$native_id = "SGD DB Id"
+
+$entrez2native = {
+  :tax =>  4932,
+  :fix => proc{|code| code.sub(/SGD:S0/,'S0') },
+  :check => proc{|code| code.match(/^S0/)},
+}
+
+$lexicon = {
+  :file => {
+    :url => "ftp://genome-ftp.stanford.edu/pub/yeast/data_download/chromosomal_feature/SGD_features.tab",
+    :native => 0,
+    :extra => [4,3,5]
+  },
+  :biomart => {
+    :database => 'scerevisiae_gene_ensembl',
+    :main => ['Entrez Gene ID', 'entrezgene'],
+    :extra => [ 
+      ['Interpro Description' , "interpro_description"], 
+    ],
+    :filter => [],
+  }
+
+}
+
+$identifiers = {
+  :file => {
+    :url => "ftp://genome-ftp.stanford.edu/pub/yeast/data_download/chromosomal_feature/SGD_features.tab",
+    :native => 0,
+    :extra => [],
+  },
+  :biomart => {
+    :database => 'scerevisiae_gene_ensembl',
+    :main => ['Entrez Gene ID', 'entrezgene'],
+    :extra => [ 
+      ['Associated Gene Name' , "external_gene_id"], 
+      ['Ensembl Gene ID', "ensembl_gene_id"  ],
+      ['Ensembl Protein ID', "ensembl_peptide_id"  ],
+      ['RefSeq Protein ID' , "refseq_peptide"] , 
+      ['UniProt/SwissProt ID' , "uniprot_swissprot"] , 
+      ['UniProt/SwissProt Accession' , "uniprot_swissprot_accession"] , 
+      ['Protein ID' , "protein_id"] , 
+      ['EMBL (Genbank) ID' , "embl"] , 
+      # Affymetrix
+      ['Affy yeast 2',"affy_yeast_2"],
+      ['Affy yg s98', "affy_yg_s98"],
+    ],
+    :filter => [],
+  }
+}
+
+$go = {
+  :url => "ftp://genome-ftp.stanford.edu/pub/yeast/data_download/literature_curation/gene_association.sgd.gz",
+  :code => 1,
+  :go   => 4,
+  :pmid => 5,
+}
+
+$query = '"saccharomyces cerevisiae"[All Fields] AND ((("proteins"[TIAB] NOT Medline[SB]) OR "proteins"[MeSH Terms] OR protein[Text Word]) OR (("genes"[TIAB] NOT Medline[SB]) OR "genes"[MeSH Terms] OR gene[Text Word]))  AND hasabstract[text] AND English[lang]'
+
+