UniProt on ActiveRecord

2006-07-11UniProt on ActiveRecord

Modeling for UniProt/Knowledgebase Entry by ActiveRecord

Examples

Loading and find Entry by name (entry_id).

$ script/console
Loading development environment.
>> Entry.find_by_name("ATAD1_HUMAN")
=> #<Entry:0x241cf5c @attributes={"name"=>"ATAD1_HUMAN", "entry_type"=>nil, "dt_create"=>"13-SEP-2005, integrated into UniProtKB/Swiss-Prot.", "dt_annotation"=>"18-APR-2006, entry version 26.", "sequence"=>"MVHAEAFSRPLSRNEVVGLIFRLTIFGAVTYFTIKWMVDAIDPTRKQKVEAQKQAEKLMKQIGVKNVKLSEYEMSIAAHLVDPLNMHVTWSDIAGLDDVITDLKDTVILPIKKKHLFENSRLLQPPKGVLLYGPPGCGKTLIAKATAKEAGCRFINLQPSTLTDKWYGESQKLAAAVFSLAIKLQPSIIFIDEIDSFLRNRSSSDHEATAMMKAQFMSLWDGLDTDHSCQVIVMGATNRPQDLDSAIMRRMPTRFHINQPALKQREAILKLILKNENVDRHVDLLEVAQETDGFSGSDLKEMCRDAALLCVREYVNSTSEESHDEDEIRPVQQQDLHRAIEKMKKSKDAAFQNVLTHVCLD", "molecular_type"=>"PRT", "sequence_length"=>"361", "id"=>"11877", "data_class"=>"STANDARD", "crc64"=>"2FAE88BA7E7140BC", "definition"=>"ATPase family AAA domain-containing protein 1.", "dt_sequence"=>"01-OCT-2002, sequence version 1.", "mw"=>"40744"}>

Accessions (AC line)

>> Entry.find_by_name("ATAD1_HUMAN").acs.map {|ac| ac.name }
=> ["Q8NBU5", "Q6P4B9", "Q8N3G1", "Q8WYR9", "Q969Y3"]

Keywords (KW line)

>> Entry.find_by_name("ATAD1_HUMAN").kws.map {|keyword| keyword.name }
=> ["ATP-binding", "Nucleotide-binding"]

Database-cross references (DR line)

>> Entry.find_by_name("ATAD1_HUMAN").drs.map {|x| x.db_name }
=> ["EMBL", "EMBL", "EMBL", "EMBL", "EMBL", "EMBL", "EMBL", "EMBL", "LinkHub", "Pfam", "InterPro", "InterPro", "InterPro", "Ensembl", "HSSP", "PROSITE", "SMART", "HGNC", "UniGene"]

Sequence

>> Entry.find_by_name("ATAD1_HUMAN").sequence
=> "MVHAEAFSRPLSRNEVVGLIFRLTIFGAVTYFTIKWMVDAIDPTRKQKVEAQKQAEKLMKQIGVKNVKLSEYEMSIAAHLVDPLNMHVTWSDIAGLDDVITDLKDTVILPIKKKHLFENSRLLQPPKGVLLYGPPGCGKTLIAKATAKEAGCRFINLQPSTLTDKWYGESQKLAAAVFSLAIKLQPSIIFIDEIDSFLRNRSSSDHEATAMMKAQFMSLWDGLDTDHSCQVIVMGATNRPQDLDSAIMRRMPTRFHINQPALKQREAILKLILKNENVDRHVDLLEVAQETDGFSGSDLKEMCRDAALLCVREYVNSTSEESHDEDEIRPVQQQDLHRAIEKMKKSKDAAFQNVLTHVCLD"

References

>> Entry.find_by_name("ATAD1_HUMAN").refs_count
=> 5
>> Entry.find_by_name("ATAD1_HUMAN").refs[0]   
=> #<Ref:0x27944a0 @rcs=[#<Rc:0x27932a8 @attributes={"text"=>"Pituitary", "token"=>"TISSUE", "id"=>"16335", "ref_id"=>"26323"}>], @attributes={"entry_id"=>"11877", "title"=>"A novel gene expressed in fetal normal pituitary.", "auther"=>"Liu F., Xu X.R., Qian B.Z., Xiao H., Chen Z., Han Z.", "id"=>"26323", "location"=>"Submitted (MAR-2001) to the EMBL/GenBank/DDBJ databases."}, @rps=[#<Rp:0x2793578 @attributes={"id"=>"31223", "ref_id"=>"26323", "comment"=>"NUCLEOTIDE SEQUENCE [MRNA]"}>], @rgs=[], @rxs=[]>

Comments (CC line)

>> Entry.find_by_name("ATAD1_HUMAN").ccs       
=> [#<Cc:0x26cd594 @attributes={"entry_id"=>"11877", "topic"=>"SIMILARITY", "id"=>"69666", "contents"=>"Belongs to the AAA ATPase family."}>]

Count Homo sapiens entries

>> Os.find_by_name("Homo sapiens")
=> #<Os:0x24940fc @attributes={"name"=>"Homo sapiens", "common_name"=>"(Human)", "id"=>"31"}>
>> Os.find_by_name("Homo sapiens").entries_count
=> 1701

uniprot_sprot.dat.gz and Rails

$ curl -O ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz
$ rails uniprot -d mysql
$ cd uniprot

Then save uniprot/Rakefile, uniprot/config/database.yml, uniprot/db/migrate/001_create_entries.rb and uniprot/app/models/entry.rb.

Importing UniProt data into database

$ rake generate
$ rake db:migrate
$ rake import

After 20 hours,

$ script/console

Have fun !

uniprot/Rakefile

ActiveRecord, UniProt |

# Add your own tasks in files placed in lib/tasks ending in .rake,
# for example lib/tasks/capistrano.rake, and they will automatically be available to Rake.

require(File.join(File.dirname(__FILE__), 'config', 'boot'))

require 'rake'
require 'rake/testtask'
require 'rake/rdoctask'

require 'tasks/rails'


desc "import data"
task :import do
  require "#{RAILS_ROOT}/config/environment"
  require 'bio'
  require 'zlib'
  io = Zlib::GzipReader.open("../uniprot_sprot.dat.gz")

  Bio::FlatFile.open(io).each do |entry|
    print entry.entry_id
    if Entry.find_by_name(entry.entry_id)
      puts "\tskipped" 
      next
    else
      $stdout.sync = true
      print "\t." 
    end

    e = Entry.new(:name            => entry.entry_id,
                  :data_class      => entry.id_line['DATA_CLASS'].to_s,
                  :molecular_type  => entry.id_line['MOLECULE_TYPE'].to_s,
                  :sequence_length => entry.id_line['SEQUENCE_LENGTH'].to_i,
                  :dt_create       => entry.dt['created'].to_s,
                  :dt_sequence     => entry.dt['sequence'].to_s,
                  :dt_annotation   => entry.dt['annotation'].to_s,
                  :definition      => entry.de)
    e.sequence = entry.seq.to_s
    e.crc64    = entry.sq['CRC64'].to_s
    e.mw       = entry.sq['MW'].to_i    

    print "."    

    entry.accessions.each do |ac|
      e.acs << Ac.new(:name => ac)
    end

    print "."

    entry.os.each do |os|
      if o = Os.find_by_name(os['os']) 
      else o = Os.new(:name => os['os'], :common_name => os['name'].to_s)
      end
      e.oss << o
    end

    print "."

    entry.oc.each_with_index do |key, level|
      if o = Oc.find_by_name(key)
      else o = Oc.new(:name => key, :level => level)
      end
      e.ocs << o
    end

    print "."

    entry.ox.each do |db_name, accs|
      accs.each do |acc|
        if o = Ox.find(:first, :conditions => ["db_name = ? AND accession = ?", 
                                               db_name, acc])
        else o = Ox.new(:db_name => db_name, :accession => acc)
        end
        e.oxs << o
      end
    end

    e.gn = Gn.new
    entry.gn.each do |g|
      unless g.class == Hash
        cannonical_key = {'ORFNames' => :orfs, 'Name' => :name, 
                          'OrderedLocusNames' => :loci}
        g2 = {}
        g.to_s.split(';').map {|x| x.strip }.each do |ge|
          key, value = ge.split('=')
          g2[cannonical_key[key]] = value
        end
        g = g2
      end
      g[:synonyms] = [] unless g[:synonyms]
      g[:name] = '' unless g[:name]
      g[:loci] = [] unless g[:loci]
      g[:orfs] = [] unless g[:orfs]
      e.gn.name = g[:name]

      g[:synonyms].map do |synonym|
        e.gn.synonyms << GnSynonym.new(:synonym => synonym)
      end
      g[:loci].each do |locus|
        e.gn.loci << GnLocus.new(:locus => locus)
      end
      g[:orfs].map do |orf|
        e.gn.orf_names << GnOrfName.new(:name => orf)
      end
    end

    print "."

    entry.ref.each do |ref|
      r = Ref.new(:title => ref['RT'],
                  :auther => ref['RA'],
                  :location => ref['RL'])
    print "."
      ref['RG'].each do |rg|
        r.rgs << Rg.new(:name => rg)
      end
    print "."
      ref['RX'].each do |key, value|
        next if value == nil
        r.rxs << Rx.new(:name => key, :identifier => value)
      end
    print "."
      ref['RP'].each do |rp|
        r.rps << Rp.new(:comment => rp)
      end
    print "."
      ref['RC'].each do |rc|
        r.rcs << Rc.new(:token => rc['Token'], :text => rc['Text'])
      end
      e.refs << r
    end

    print "."

    entry.cc.each do |k, v|
      [entry.cc(k)].flatten.each do |value|
        e.ccs << Cc.new(:topic => k, 
                        :contents => value) 
      end
    end

    print "."

    entry.dr.each do |db_name, vs|
      vs.each do |v|
        e.drs << Dr.new(:db_name   => db_name, 
                        :entry_name => v[0], 
                        :content1   => v[1].to_s, 
                        :content2   => v[2].to_s, 
                        :content3   => v[3].to_s)
      end
    end

    print "."

    entry.kw.each do |key|
      if kw = Kw.find_by_name(key)
      else kw = Kw.new(:name => key) 
      end
      e.kws << kw
    end

    entry.ft.each do |name, fts|
      fts.each do |ft|
        e.fts << Ft.new(:name => name,
                        :from => ft['From'],
                        :to => ft['To'],
                        :description => ft['Description'],
                        :ftid => ft['FTId'])
      end
    end

    print "."

    e.save

    puts 'done'
  end
end

desc "mysql create database"
task :create do
  sh "mysqladmin5 -uroot drop uniprot_development"
  sh "mysqladmin5 -uroot create uniprot_development"
end

uniprot/config/database.yml

ActiveRecord, UniProt |

development:
   adapter: mysql
   database: uniprot_development
   username: root
   password:
   host: localhost

uniprot/db/migrate/001_create_entries.rb

ActiveRecord, UniProt |

class CreateEntries < ActiveRecord::Migration
  def self.up
    create_table(:entries) do |t|
      t.column(:name, :string)
      t.column(:data_class, :string)
      t.column(:molecular_type, :string)
      t.column(:sequence_length, :integer)
      t.column(:entry_type, :string)
      t.column(:dt_create, :string)
      t.column(:dt_sequence, :string)
      t.column(:dt_annotation, :string)
      t.column(:definition, :string)
      t.column(:sequence, :text)
      t.column(:mw, :integer)
      t.column(:crc64, :string)
    end
    add_index(:entries, :name)

    create_table(:acs) do |t|
      t.column(:entry_id, :string)
      t.column(:name, :string)
    end
    add_index(:acs, :name)
    add_index(:acs, :entry_id)

    create_table(:gns) do |t|
      t.column(:name, :string)
      t.column(:entry_id, :string)
    end
    add_index(:gns, :name)
    add_index(:gns, :entry_id)

    create_table(:gn_synonyms) do |t|
      t.column(:gn_id, :integer)
      t.column(:synonym, :integer)
    end
    add_index(:gn_synonyms, :synonym)
    add_index(:gn_synonyms, :gn_id)

    create_table(:gn_loci) do |t|
      t.column(:gn_id, :integer)
      t.column(:locus, :integer)
    end
    add_index(:gn_loci, :locus)
    add_index(:gn_loci, :gn_id)

    create_table(:gn_orf_names) do |t|
      t.column(:gn_id, :integer)
      t.column(:name, :integer)
    end
    add_index(:gn_orf_names, :name)
    add_index(:gn_orf_names, :gn_id)

    create_table(:entries_oss, :id => false) do |t|
      t.column(:entry_id, :integer)
      t.column(:os_id, :integer)
    end
    add_index(:entries_oss, :entry_id)
    add_index(:entries_oss, :os_id)

    create_table(:oss) do |t|
      t.column(:name, :string)
      t.column(:common_name, :string)
    end
    add_index(:oss, :name)

    create_table(:entries_ocs, :id => false) do |t|
      t.column(:entry_id, :integer)
      t.column(:oc_id, :integer)
    end
    add_index(:entries_ocs, :entry_id)
    add_index(:entries_ocs, :oc_id)

    create_table(:ocs) do |t|
      t.column(:level, :integer)
      t.column(:name, :string)
    end
    add_index(:ocs, :name)

    create_table(:entries_oxs, :id => false) do |t|
      t.column(:entry_id, :integer)
      t.column(:ox_id, :integer)
    end
    add_index(:entries_oxs, :entry_id)
    add_index(:entries_oxs, :ox_id)

    create_table(:oxs) do |t|
      t.column(:db_name, :string)
      t.column(:accession, :string)
    end
    add_index(:oxs, :db_name)
    add_index(:oxs, :accession)

    # references
    create_table(:refs) do |t|
      t.column(:entry_id, :integer)
      t.column(:title, :string)
      t.column(:auther, :string)
      t.column(:location, :string)
    end
    add_index(:refs, :location)
    add_index(:refs, :entry_id)
    create_table(:rxs) do |t|
      t.column(:name, :string)
      t.column(:identifier, :string)
      t.column(:ref_id, :integer)
    end
    add_index(:rxs, :name)
    create_table(:rgs) do |t|
      t.column(:name, :string)
      t.column(:ref_id, :integer)
    end
    add_index(:rgs, :name)
    create_table(:rps) do |t|
      t.column(:comment, :string)
      t.column(:ref_id, :integer)
    end
    add_index(:rps, :comment)
    create_table(:rcs) do |t|
      t.column(:token, :string)
      t.column(:text, :string)
      t.column(:ref_id, :integer)
    end
    add_index(:rcs, :token)

    create_table(:ccs) do |t|
      t.column(:topic, :string)
      t.column(:contents, :text)
      t.column(:entry_id, :string)
    end
    add_index(:ccs, :entry_id)
    add_index(:ccs, :topic)
    
    create_table(:drs) do |t|
      t.column(:entry_id, :string)
      t.column(:db_name, :string)
      t.column(:entry_name, :string)
      t.column(:content1, :string)
      t.column(:content2, :string)
      t.column(:content3, :string)
    end
    add_index(:drs, :entry_id)
    add_index(:drs, :db_name)
    add_index(:drs, :entry_name)

    create_table(:entries_kws, :id => false) do |t|
      t.column(:entry_id, :integer)
      t.column(:kw_id, :integer)
    end
    add_index(:entries_kws, :entry_id)
    add_index(:entries_kws, :kw_id)

    create_table(:kws) do |t|
      t.column(:name, :string)
    end
    add_index(:kws, :name)

    create_table(:fts) do |t|
      t.column(:entry_id, :string)
      t.column(:name, :string)
      t.column(:from, :string)
      t.column(:to, :string)
      t.column(:description, :string)
      t.column(:ftid, :string)
    end
    add_index(:fts, :entry_id)
    add_index(:fts, :name)
    add_index(:fts, :ftid)
  end

  def self.down
    drop_table :entries
    drop_table :acs
    drop_table :gns
    drop_table :gn_synonyms
    drop_table :gn_loci
    drop_table :gn_orf_names
    drop_table :ccs
    drop_table :drs
    drop_table :kws
    drop_table :fts
  end
end

uniprot/app/models/entry.rb

ActiveRecord, UniProt |

es_oxs

コメントを書く

トラックバック - http://bioruby.g.hatena.ne.jp/nakao_mitsuteru/20060711

"aac".translate #=> "N"

2006-07-11UniProt on ActiveRecord

Modeling for UniProt/Knowledgebase Entry by ActiveRecord

Examples

Loading and find Entry by name (entry_id).

Accessions (AC line)

Keywords (KW line)

Database-cross references (DR line)

Sequence

References

Comments (CC line)

Count Homo sapiens entries

uniprot_sprot.dat.gz and Rails

Importing UniProt data into database

uniprot/Rakefile

uniprot/config/database.yml

uniprot/db/migrate/001_create_entries.rb

uniprot/app/models/entry.rb