bio 0.7.0

data/doc/Design.rd.ja

@@ -0,0 +1,341 @@
+=begin
+
+  $Id: Design.rd.ja,v 1.7 2002/07/02 01:40:24 k Exp $
+
+  Copyright (C) 2001 KATAYAMA Toshiaki <k@bioruby.org>
+
+= BioRuby �γ�ȯ���ˤȥǥ�����
+
+�������⥸�塼����ɲä������ CVS �ΰʲ��Υ�ݥ��ȥ�ˡ����Ƥ˽��ä�
+Ŭ�ڤ� commit ���ޤ����᡼��󥰥ꥹ�Ȥʤɤ� contribute ���줿�����ɤ�
+�ܿͤ� committer �ˤʤäƤ�餦���������åդ� commit ���ޤ���
+
+  bioruby/
+  |-- README            �Ϥ����
+  |-- install.rb        ���󥹥ȡ���
+  |-- COPYING
+  |-- COPYING.LIB
+  |-- bin/              ���ץꥱ�������
+  |-- lib/              Ruby �ǽ񤫤줿�饤�֥��
+  |   `-- bio/            ����ʤɴ���Ū�ʥ��饹
+  |       |-- data/         ��ʪ��Ū������ʤɥǡ������Τ��
+  |       |-- db/           �Ƽ�ǡ����١����ѡ���
+  |       |-- io/           �ǡ�����������
+  |       `-- appl/         �������ץ�ν���
+  |-- doc/              �ɥ������
+  |-- ext/              C �ǽ񤫤줿�饤�֥��
+  `-- sample/           ����ץ륳����
+
+== Ruby ��ʬ�ˤĤ��ƤΥǥ������bioruby/lib/bio/ �ʲ���
+
+����ޤǤ˹Ԥʤ�줿�����Υǥ����󥳥󥻥ץȤȡ���������ˤʤɤˤĤ��Ƥ�
+�Ȥ�Ƥ����ޤ���
+
+BioRuby �������饹�� module Bio �ǰϤळ�Ȥǡ�̾�����֤��ڤ�ʬ������ˤ�
+�ޤ���
+
+=== lib/bio/ �ǡ�����¤��
+
+����䥢�ߥλ�������ʸ�����󡢰����Ҥ� location �� feature������դʤ�
+����ݥǡ�����¤�򰷤����饹�� lib/bio/ ľ�������֤��Ƥ��ޤ��������ϳ�
+�ǡ����١������ѡ����ʤɤ����ľ�ܸƤФ�ޤ���
+
+¾�ˡ����饤���ȥ��饹�ʤɤμ�����ɬ�פ����Τ�ޤ��󡣤ޤ�����ʪ��η�
+��ʬ���ɽ�� Taxonomy ���饹�� GeneOntology �ʤɤΥ��饹�⤢�����������
+�Τ�ޤ���
+
+=== lib/bio/db/ �ǡ����١������ѡ�����
+
+�Ȥ����δ�ñ�� vs ������ʣ�������������ᤵ vs ����νŤ����ʤɥХ��
+�������ɬ�������ɤ��Ȥϸ����ʤ����⤢��ޤ�����lib/bio/db.rb �Ǥϰʲ�
+�Τ褦���ȼ��Υ����ǥ��ʤ��Ǥ�Ʊ�ͤʻ�ߤ��ʤ���Ƥ������ɤ�����Ĵ�٤Ƥ�
+�ޤ���ˤ���Ѥ��Ƥ��ޤ����������ѡ������ɲä�����⻲�ͤˤ��Ʋ�������
+
+  ����ȥ�      ���줾��Υǡ����١����ˤ����룱�ĤΥǡ���ñ��
+                ��) GenBank �ʤ� LOCUS ���� // �ޤǤ����Ƥι�
+  �ǥ�ߥ�      ����ȥ�ȥ���ȥ����ڤ�ʸ����
+                ��) GenBank �ʤ� // �����ι�
+  ����          ����ȥ�κ�ü�������ʤɤ˵������ȥåץ�٥�μ��̻�
+                ��) GenBank �ʤ� DEFINITION �� FEATURES �ʤ�
+  �ե������    ������˰�̣�Τ���ñ�̤�ʤ�ʣ���Ԥ���ʤ�֥��å�
+                ��) GenBank �ʤ� SOURCE �˴ޤޤ�� taxonomy �ޤǤι������ʤ�
+
+BioRuby �Υǡ����١������ѡ����ϡ�������ȥ�ʬ��ʸ����� .new ���Ϥ�����
+�ѡ���������̤��ݻ����륤�󥹥��󥹤��֤��ǥ�����ˤʤäƤ��ޤ����ƥǡ�
+���١������饨��ȥ�ñ�̤Υǡ�����������ˡ�ϡ��긵�Υե�åȥե�������
+����硢�ͥåȱۤ��� DBGET �� BioFetch ������硢NCBI �����äƤ�����硢
+�ʤɻȤ����ˤ�ä��͡��Ǥ������ɤ����饨��ȥ�������� (io) �˴ؤ�餺��
+�ѡ����ϥ���ȥ��ѡ��������������ǰ�Ǥ��ޤ���
+
+�ǽ�Ū�ˤ����ƤΥǡ����Ϥ��餫����ѡ������� tab �ڤ�Υǡ������ڤ��ߡ�
+MySQL �ʤɤ��ͤù���Ǥ��ޤäƥѡ�����ɬ�פ��ʤ��褦�������ˤ������Ǥ���
+BioPerl �� BioPerl-DB �˻��Ƥ���Ȼפ��ޤ�����BioRuby ɸ��� DataBase ��
+�������Ȥ� BioRuby-DB (class BRDB) �Ȥ��Ƴ�ȯ��ʤ�Ƥ��ޤ���BioRuby ��
+���������Ȥ� BioHackathon �� BOSC �˻��ä��� OBDA �� BioSQL �ʤɤ˽��
+��褦�ˤʤ�ޤ����Τǡ�������ȼ��ǡ����١�����ɬ�פ���ʬ�ϸ��äƤ�����
+�⤷��ޤ���
+
+  * OBDA : Open Bio Sequence Database Access
+    * ((<URL:http://obda.open-bio.org/>))
+    * ((<URL:http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/?cvsroot=obf-common>))
+  * BOSC : Bioinformatics Open Source Conference
+    * ((<URL:http://bosc.open-bio.org/>))
+
++ �ǡ����١�����¤����ݲ�
+
+lib/bio/db/ �ʲ��Υ⥸�塼��ϡ�lib/bio/db.rb �� require �������ʤ��Ȥ�
+DB ���饹��Ѿ����ޤ�������ˡ������Ĥ��Υǡ����١���������ι�¤�����
+�Ƥ��뤿�ᡢ�Ȥꤢ���� NCBI ����KEGG ��ޤ�ˡ�EMBL ����ʬ���ơ��ѡ�����
+�ݤ˶��̤ǻȤ���᥽�åɤ�ͭ���褦�Ȥ��Ƥ��ޤ������������ºݤˤϤ����
+�η��������ƤϤޤ�ʤ��ǡ����١�����¿���Τǡ�DB ������Ѿ�������⤢
+��Ǥ��礦��
+
++ �ե�����ɤ��Ф��붦�̤� API �����
+
+�͡��ʥǡ����١����Ǥ褯���̤��Ƹ����褦�ʥե�����ɤ��Ф��Ƥϡ�db.rb
+��ˤ���ɥ�����ȤǼ�����붦�̤Υ᥽�å�̾��Ȥäơ��ǡ����������
+��褦�ˤ��ޤ���
+
+���Τ褦�ˡ��ե�����ɤ��Ф��붦�̤Υ᥽�å�̾�����ƥǡ����١����Υѡ���
+��Ŭ�ڤ˼�������Ƥ���С��ǡ����١�����˥᥽�åɤ�Ф���ɬ�פ�����ޤ���
+�㤨�С��ǡ����١������ۤʤäƤ�֥���ȥ�������ե�����ɡ׼����Τ����
+�᥽�åɤ� definition �������ȿ�¬���䤹���ʤ�ޤ���
+
++ ɬ�פʻ��ޤǥѡ������٤餻���on-demand parsing��
+
+GenBank �ʤ�ʣ���ʹ�¤�Υǡ����١�����ѡ�������ݤˤ⥹�롼�ץåȤ��ɤ�
+���뤿�ᡢ�ǽ�ϥե����������ڤ�ʬ����������������Ԥʤ�������Υե���
+�����Υǡ������׵᤹��᥽�åɤ��ƤФ줿�������ºݤ˥ե��������Υǡ�
+����٤����ѡ������������Ԥʤ��ޤ���������󤳤λ��ѡ��������Τϡ�ɬ
+�פʥե�����ɤ����Ǥ���
+
++ ���٥ѡ���������̤ϥ���å��夷�Ƥ���
+
+�嵭�� on-demand parsing �ǥѡ���������̤ϡ����֥���������˥���å���
+���Ƥ����Τǡ������ܰʹߤΥ᥽�åɥ�����Ǥ��ݻ����Ƥ���ѡ����ѤߤΥǡ�
+�����֤��ޤ�������ˤ��Ť��ѡ����򷫤��֤��褦�ʥ����С��إåɤ�̵����
+�Ƥ��ޤ���
+
+=== lib/bio/data/ ������ǡ�����
+
+lib/bio/data/ �ʲ��ˡ������Ĥ��Υǡ����ʥ��ߥλ���̾����KEGG �Ǥ���ʪ��
+̾�����ɥ�ɽ�ʤɡˤ�����Ȥ����֤���Ƥ��ޤ���
+
+  Bio::AminoAcid �� ���ߥλ���̾����ɽ���ϥå��塢�ʤ�
+
+�����ϡ�ɬ�פʥ��饹�˥��������᥽�åɤ�������Ƥ��ɤ��Ǥ��礦��
+
+=== lib/bio/io/ ���󥿡��ե�������IO ��
+
+lib/bio/io/ �ʲ��ˤϡ��ե�åȥե���������򥨥�ȥ�ñ�̤��ɤ߹��९�饹��
+���Υ�ͥåȤ���ǡ���������Ԥʤ� DBGET ���饹�� NCBI �� PubMed �ˤ�� 
+MEDLINE �ǡ���������Ԥʤ� PubMed ���饹��OBDA �˽�򤷤� BioRegistry,
+BioFetch, BioSQL �ʤɤˤ��ǡ���������Ԥ����饹�ʤɤ�����ޤ���
+
+* flatfile.rb �ʼ����ѡ�
+
+    # ��������Υե������ GenBank �ե����ޥåȤȤ��Ƴ���
+    flatfile = Bio::FlatFile.open(Bio::GenBank, "genbank/gbest40.seq")
+
+    # �ޤ��ϥե�����ϰ�����Ϳ����
+    Bio::FlatFile.new(Bio::GenBank, ARGF)
+
+    # �ޤ��� IO ��Ϳ����
+    Bio::FlatFile.new(Bio::GenBank, IO.popen("gzip -dc nc1101.flat.gz"))
+
+    # �ǽ�Υ���ȥ�� GenBank ���֥������Ȥ�
+    gb = flatfile.next_entry
+
+    # ����ȥꤴ�Ȥ� Bio::GenBank ���֥������Ȥ�����
+    flatfile.each do |gb|
+      puts gb.definition
+    end
+
+=== lib/bio/appl/ �ġ����
+
+FASTA(SSEARCH), [PSI-]BLAST, HMMER, CLUSTALW �ʤɤγ������ץ��Ȥä���
+����Ԥ��ޤ�����������ʼ¹ԡ�http �ʤɤˤ���⡼�ȼ¹ԡ���̤Υե���
+�ޥåȤʤɤ�ռ������ˡ���̤��ѡ��������Ǽ���줿 Report ���֥������Ȥ�
+�ɤ��֤�褦�ʴ����ˤ��Ƥ����ޤ���
+
+* query �Ȥʤ륪�֥������Ȥˡ����ץ��¹Ԥ���᥽�åɤ������ɬ�פʰ���
+  ��Ϳ�����
+
+    factory = Bio::Fasta.remote('fasta', 'genes')
+    fa_res = f.fasta(factory)   # f �� Bio::FastaFormat ���֥�������
+    fa_res = seq.fasta(factory) # seq �� Bio::Sequence::AA ���֥������Ȥʤ�
+
+* ���������������ե����ȥ�ˡ������С�query��target �ʤɤ����ꤷ�ơ�����
+  ���¹Ԥ���᥽�åɤ�Ƥ�
+
+    factory = Bio::Fasta.local(prog, target, opt)
+    fa_res = factory.query(seq)
+
+�ʤɤ����Ĥ��μ�����ˡ���ͤ����ޤ���Bio::Fasta, Bio::Blast �Ǥ�ξ����
+����ץꤷ�Ƥ��ޤ��ˡ�
+
+�ե����ȥ��᥽�åɤؤΥ��ץ������Ϥ����ϡ�ʣ����ʪ�ϥ���ܥ�򥭡���
+���� hash �ˤ��������ɤ����⤷��ޤ��󡣤⤷����̾���Ĥ������Ԥ���
+
+    res = a.query(:hoge => fuga, :hoge2 => fuga2)
+
+����¾�Υ��ץ�Υ��󥿡��ե�������������ʤ�����ͤ���Ƥ��������Ȼ�
+���ޤ���
+
+== �����ǥ��󥰥�������
+
+���饹�߷ס��᥽�å�����ʤ����̤ˤ����ơ�KISS (keep it simple stupid) ��
+���ܤǤ������������ʤ�Ǥ⤫��Ǥ� class ��ʬ�򤷤Ƥ��ޤ����ɤ��櫓�Ǥ�
+�ʤ��Ǥ��礦����ǰ�Ȥ��ư�ĤΤޤȤޤ���Ȼפ����Τޤ�ʬ�򤹤�Ф褯��
+�ä˻Ȥ��󤷤Τ����ʤ����֥������Ȥ���������ɬ�פϤʤ��Ȼפ��ޤ���
+
+����Ū�ʻ��ˤĤ��Ƥϡ���˲�����;�Ϥ�����Ȼפ��ޤ����񤭴�������ˤ��
+����ץ��ʬ����䤹���ʤ��硢����γ�ȯ�����ࡼ���ˤʤ�Ȼפ�����
+�ˤϡ��ɤ�ɤ������Ƥ����ޤ����դˡ�¿����Ψ���ɤ��ʤ�Ȥ��Ƥⲿ����
+�Ƥ��뤫ʬ����ˤ����ʤ��硢ɬ�������⤤�Ȼפ����Ѷ�Ū����ͳ�����Ĥ���
+�ʤ����Ϻ��Ѥ򸫹�碌�뤳�Ȥ⤢��Ȼפ��ޤ���������ˤ��Ƥ⡢�С�����
+�� 1.0 �ޤǤϲ��̸ߴ��������ˤ����ѹ���Ԥʤ�ͽ��Ǥ���
+
+��������������ˤ����ܸ�ʤ��� ASCII ��ʸ����ϴޤޤʤ��褦�ˤ��ޤ���
+
+=== �إå���
+
+�إå����ˤϡ��ե�����̾�����ס�����ԡ��饤���󥹡�CVS �� ID ��񤭤ޤ�
+�ʲ�����Ǥ� ID �Ρ��Ÿ������ʤ��褦�����Ѥˤ��Ƥ��ޤ������ºݤ� $ �Ǥ��ˡ�
+
+    #
+    # bio/hoge.rb - biological hoge class
+    #
+    #   Copyright (C) 2000, 2001 KATAYAMA Toshiaki <k@bioruby.org>
+    #
+    #  This library is free software; you can redistribute it and/or
+    #  modify it under the terms of the GNU Lesser General Public
+    #  License as published by the Free Software Foundation; either
+    #  version 2 of the License, or (at your option) any later version.
+    #
+    #  This library is distributed in the hope that it will be useful,
+    #  but WITHOUT ANY WARRANTY; without even the implied warranty of
+    #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+    #  Lesser General Public License for more details.
+    #
+    #  You should have received a copy of the GNU Lesser General Public
+    #  License along with this library; if not, write to the Free Software
+    #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+    #
+    #  ��Id:��
+    #
+
+���ץꥱ�������䥵��ץ륳���ɤ�񤯾��ϡ�ruby �Υѥ��˰�¸���ʤ���
+���ˣ����ܤ�
+
+    #!/usr/bin/env ruby
+
+�Τ褦�˻Ϥ��Τ��ɤ��Ǥ��礦��
+
+=== ����
+
+���Τ� module Bio �dz�ꡢɬ�פʥ��饹��������ޤ���������Ǥ� # ��Ȥ�
+�ƥ����Ȥ�Ĥ���RD ��Ȥä������Ȥϥե�����κǸ�Υɥ����������
+�ǤϽФƤ��ʤ��褦�ˤ��ޤ����⤷�������륯�饹�� bio/db/ �ʲ��Υǡ����١�
+���ѡ����Ϥ��ä��顢bio/db.rb �Υɥ�����Ȥ⻲�Ȥ��Ʋ�������
+
+    require 'foo/bar'
+
+    modlue Bio
+
+      class Hoge
+
+        # this method do hogehoge
+        def hoge(fuga)
+          @fuga = fuga		# storing data fuga
+        end
+
+        def gege
+        end
+
+      end
+
+    end
+
+RDoc ��Ȥ��Х��饹��᥽�åɤξ�˽񤫤줿�����Ȥ��� HTML �ʤɤ�����
+�Ǥ���褦�Ǥ������� ri �Ѥν��Ϥ�Ǥ���褦�ˤʤäƤ����顢���Ѥ��뤫��
+����ޤ���
+
+=== �ƥ��ȥ�������
+
+�ƥ��ȥ����ɤϥ��饹����ʤ�������ʬ�Τ��Ȥˤ�Ĥ��뤳�Ȥˤ��ޤ����ƥ���
+�����ɤν����Ϥ��줫�鸡Ƥ���Ƥ���ɬ�פ�����ޤ������Ȥꤢ�����ʲ��Τ�
+���ʹ�ʸ�ǥƥ��ȥ����ɤ�Ϥߤޤ���
+
+    if __FILE__ == $0
+      # test code here
+    end
+
+���Τ��ޤ��ʤ��Τ褦�ʹ�ʸ�ϡ��ե����� hoge.rb �����ޥ�ɥ饤�󤫤�
+
+    % ruby hoge.rb
+
+�ʤɤȥ�����ץȤȤ��Ƶ�ư���줿���˼¹Ԥ���ޤ������饤�֥��Ȥ���
+
+    require 'hoge'
+
+�Τ褦�˥����ɤ��줿���ˤϼ¹Ԥ���ʤ��褦�ˤ��뤿��ξ����Ǥ���
+
+�ƥ��Ȥ���ˡ�ϡ�Test::Unit �� ruby ��ɸ��饤�֥��Ȥ���ź�դ����褦
+�ˤʤ�к��Ѥ��Ƥ⤤���Ȼפ��ޤ���������ޤǤϿ���������Ȼפ��ޤ�����
+���Ȥ˳����ե������ͥåȥ���ʤɤ�ɬ�פʾ��ɤ����뤫�Ȥ������󥹥ȡ�
+������ư���ǧ�Ȥ��ƥƥ��Ȥ�¹Ԥ�����ˡ�ʤɤ⸡Ƥ����ɬ�פ�����ޤ���
+
+=== �ɥ��������
+
+����ޤǡ��ƥ��饹�ˤĤ��Ƥϡ����ޤ�ɥ�����Ȳ�����Ƥ��ޤ���Ǥ�������
+����ϥƥ��ȥ����ɤΤ��ȡ��ե�����κǸ����� RD �ǥ᥽�åɤʤɤΥɥ����
+��Ȥ��ɲä��뤳�Ȥˤ��Ƥ����ޤ���
+
+    =begin
+
+    = Bio::Hoge
+
+    Hoge ���饹�γ���������
+
+    --- Bio::Hoge.new(fuga)
+
+          ���饹�᥽�åɤ�������
+
+    --- Bio::Hoge#to_a
+
+          �᥽�åɤ�������
+
+    == Bio::Hoge::Fuga
+
+    �������饹 Hoge::Fuga �γ�������
+
+    --- Bio::Hoge::Fuga.new(fuga)
+
+          ���饹�᥽�åɤ�������
+
+    --- Bio::Hoge::Fuga#to_a
+
+          �᥽�åɤ�������
+
+    =end
+
+��������
+
+* ����������ˤ� ASCII �ʳ���ʸ��������ʤ����ˤΤ��ᡢ���ܸ�Υɥ����
+  ��Ȥϡ�������ʬ�ǤϤʤ��̥ե�����˵��Ҥ���doc/ �ǥ��쥯�ȥ�ʲ�����
+  ���ʤɤ��ޤ������κݡ���ĥ�Ҥ� .ja ���դ��ơ��ե�����̾��������ܸ��
+  ʬ����褦�ˤ��ޤ���
+
+* ���ҤΤ褦�ˡ�������������������Ǥ� RD �ˤ��ɥ�����Ȥ϶ػߤ��ޤ���
+  ��ͳ�Ͻ��˥����ɤ��ɤߤŤ餯�ʤ뤫��Ǥ������������ # ��Ȥä�ɬ��
+  �ʥ����Ȥ��ɲä�����ϴ��ޤ��ޤ���(���ҤΤ褦�� RDoc ���ˤ��뤫��
+  ����ޤ���)
+
+== ��ȯ�˻��ä���ˤ�
+
+BioRuby �Υ����֥����� ((<URL:http://bioruby.org>)) �򸫤ơ��᡼��󥰥�
+���Ȥ˻��ä��뤫�������å� <staff@bioruby.org> ��Ϣ�����Ƥ���������
+
+=end
+

data/doc/KEGG_API.rd

@@ -0,0 +1,1437 @@
+=begin
+
+  $Id: KEGG_API.rd,v 1.1 2005/08/31 13:29:01 k Exp $
+
+    Copyright (C) 2003-2005 Toshiaki Katayama <k@bioruby.org>
+
+= KEGG API
+
+KEGG API is a web service to use the KEGG system from your program via
+SOAP/WSDL.
+
+We have been making the ((<KEGG|URL:/kegg/>)) system available at
+((<GenomeNet|URL:/>)).  KEGG is a suite of databases including GENES,
+SSDB, PATHWAY, LIGAND, LinkDB, etc.  for genome research and related
+research areas in molecular and cellular biology.  These databases and
+associated computation services are available via WWW and the user
+interfaces are built on web browsers.  Thus, the interfaces are
+designed to be accessed by humans, not by machines, which means that
+it is troublesome for the researchers who want to use KEGG in an
+automated manner.  Besides, from the database developer's side, it is
+impossible to prepare all the CGI programs that satisfy a variety of
+users' needs.
+
+In recent years, the Internet technology for
+application-to-application communication referred to as the
+((<web service|URL:http://www.oreillynet.com/lpt/a/webservices/2002/02/12/webservicefaqs.html>))
+is improving at a rapid rate. For exmaple, Google, a popular Internet
+search engine, provides the web service called the
+((<Google Web API|URL:http://www.google.com/apis/>)).
+The service enables users to
+develop software that accesses and manipulates a massive amount of web
+documents that are constantly refreshed. In the field of genome
+research, a similar kind of web service called
+((<DAS|URL:http://www.biodas.org/>)) (distributed annotation system)
+has been used on several web sites, including
+((<Ensembl|URL:http://www.ensembl.org/>)),
+((<Wormbase|URL:http://www.wormbase.org/>)),
+((<Flybase|URL:http://www.flybase.org/>)),
+((<SGD|URL:http://www.yeastgenome.org/>)),
+((<TIGR|URL:http://www.tigr.org/>)).
+
+With the background and the trends noted above, we have started developing
+a new web service called KEGG API using 
+((<SOAP|URL:http://www.w3.org/TR/SOAP/>)) and
+((<WSDL|URL:http://www.w3.org/TR/wsdl20/>)).
+The service has been tested with
+((<Ruby|URL:http://www.ruby-lang.org/>))
+(Ruby 1.8.2 or Ruby 1.6.8 with
+((<SOAP4R|URL:http://raa.ruby-lang.org/project/soap4r/>))
+version 1.4.8.1) and
+((<Perl|URL:http://www.perl.org/>))
+(((<SOAP::Lite|URL:http://www.soaplite.com/>)) version 0.55) languages.
+Although the service has not been tested with clients written in other
+languages, it should work if the language can treat SOAP/WSDL.
+
+The ((<BioRuby|URL:http://bioruby.org/>)) project prepared a Ruby
+library to handle the KEGG API, so users of the Ruby language should
+check out the latest release of the BioRuby distribution.
+
+For the general information on KEGG API, see the following
+page at GenomeNet:
+
+  * ((<URL:http://www.genome.jp/kegg/soap/>))
+
+== Table of contents
+
+* ((<Introduction>))
+* ((<KEGG API Quick Start>))
+  * ((<Quick Start with Perl>))
+    * ((<Perl FAQ>))
+  * ((<Quick Start with Ruby>))
+  * ((<Quick Start with Python>))
+  * ((<Quick Start with Java>))
+* ((<KEGG API Reference>))
+  * ((<WSDL file>))
+  * ((<Terminology>))
+  * ((<Returned values>))
+    * ((<SSDBRelation>)), ((<ArrayOfSSDBRelation>))
+    * ((<MotifResult>)), ((<ArrayOfMotifResult>))
+    * ((<Definition>)), ((<ArrayOfDefinition>))
+    * ((<LinkDBRelation>)), ((<ArrayOfLinkDBRelation>))
+  * ((<Methods>))
+    * ((<Meta information>))
+      * ((<list_databases>)),
+        ((<list_organisms>)),
+        ((<list_pathways>))
+    * ((<DBGET>))
+      * ((<binfo>)),
+        ((<bfind>)),
+        ((<bget>)),
+        ((<btit>))
+    * ((<LinkDB>))
+      * ((<get_linkdb_by_entry>))
+    * ((<SSDB>))
+      * ((<get_best_best_neighbors_by_gene>)),
+        ((<get_best_neighbors_by_gene>)),
+        ((<get_reverse_best_neighbors_by_gene>)),
+        ((<get_paralogs_by_gene>))
+#     * ((<get_neighbors_by_gene>)),
+#       ((<get_similarity_between_genes>))
+    * ((<Motif>))
+      * ((<get_motifs_by_gene>)),
+        ((<get_genes_by_motifs>))
+    * ((<KO, OC, PC>))
+      * ((<get_ko_by_gene>)),
+        ((<get_ko_by_ko_class>)),
+        ((<get_genes_by_ko_class>)),
+        ((<get_genes_by_ko>)),
+        ((<get_oc_members_by_gene>)),
+        ((<get_pc_members_by_gene>))
+#       ((<get_ko_members>)),
+    * ((<PATHWAY>))
+      * ((<mark_pathway_by_objects>)),
+        ((<color_pathway_by_objects>)),
+        ((<get_html_of_marked_pathway_by_objects>)),
+        ((<get_html_of_colored_pathway_by_objects>))
+      * ((<get_genes_by_pathway>)),
+        ((<get_enzymes_by_pathway>)),
+        ((<get_compounds_by_pathway>)),
+        ((<get_glycans_by_pathway>)),
+        ((<get_reactions_by_pathway>)),
+        ((<get_kos_by_pathway>))
+      * ((<get_pathways_by_genes>)),
+        ((<get_pathways_by_enzymes>)),
+        ((<get_pathways_by_compounds>)),
+        ((<get_pathways_by_glycans>)),
+        ((<get_pathways_by_reactions>)),
+        ((<get_pathways_by_kos>))
+      * ((<get_linked_pathways>))
+      * ((<get_genes_by_enzyme>)),
+        ((<get_enzymes_by_gene>))
+      * ((<get_enzymes_by_compound>)),
+        ((<get_enzymes_by_glycan>)),
+        ((<get_enzymes_by_reaction>)),
+        ((<get_compounds_by_enzyme>)),
+        ((<get_compounds_by_reaction>)),
+        ((<get_glycans_by_enzyme>)),
+        ((<get_glycans_by_reaction>)),
+        ((<get_reactions_by_enzyme>)),
+        ((<get_reactions_by_compound>)),
+        ((<get_reactions_by_glycan>))
+    * ((<GENES>))
+      * ((<get_genes_by_organism>))
+    * ((<GENOME>))
+      * ((<get_number_of_genes_by_organism>))
+    * ((<LIGAND>))
+      * ((<convert_mol_to_kcf>))
+
+== Introduction
+
+This guide explains how to use the KEGG API in your programs for 
+searching and retrieving data from the KEGG database.
+
+== KEGG API Quick Start
+
+As always, the best way to become familar with it is by looking at an
+example.  In this document, sample codes written in several languages
+are shown.  After understanding the first exsample, try other APIs.
+
+Firstly, you have to install the SOAP related libraries for the
+programming language of your choice.
+
+
+=== Quick Start with Perl
+
+In the case of Perl, you need to install the following packages:
+
+  * ((<SOAP Lite|URL:http://soaplite.com/>))
+  * ((<MIME-Base64|URL:http://search.cpan.org/author/GAAS/MIME-Base64/>))
+  * ((<LWP|URL:http://search.cpan.org/author/GAAS/libwww-perl/>))
+  * ((<URI|URL:http://search.cpan.org/author/GAAS/URI/>))
+
+Here's a first example in Perl language.
+
+  #!/usr/bin/env perl
+  
+  use SOAP::Lite;
+  
+  $wsdl = 'http://soap.genome.jp/KEGG.wsdl';
+  
+  $serv = SOAP::Lite->service($wsdl);
+  
+  $start = 1;
+  $max_results = 5;
+  
+  $top5 = $serv->get_best_neighbors_by_gene('eco:b0002', $start, $max_results);
+  
+  foreach $hit (@{$top5}) {
+    print "$hit->{genes_id1}\t$hit->{genes_id2}\t$hit->{sw_score}\n";
+  }
+
+The output will be
+
+  eco:b0002       eco:b0002       5283
+  eco:b0002       ecj:JW0001      5283
+  eco:b0002       sfx:S0002       5271
+  eco:b0002       sfl:SF0002      5271
+  eco:b0002       ecc:c0003       5269
+
+showing that eco:b0002 has Smith-Waterman score 5271 with sfl:SF0002
+as a 4th hit among the entire KEGG/GENES database (here, "eco" means
+E. coli K-12 MG1655 and "sfl" means Shigella flexneri 2457T in the
+KEGG organism codes).
+
+The method internally searches the KEGG/SSDB (Sequence Similarity
+Database) database which contains information about the amino acid
+sequence similarities among all protein coding genes in the complete
+genomes, together with information about best hits and bidirectional
+best hits (best-best hits).  The relation of gene x in genome A and
+gene y in genome B is called bidirectional best hits, when x is the
+best hit of query y against all genes in A and vice versa, and it is
+often used as an operational definition of ortholog.
+
+Next example simply lists PATHWAYs for E. coli ("eco") in KEGG
+database.
+
+  #!/usr/bin/env perl
+
+  use SOAP::Lite;
+
+  $wsdl = 'http://soap.genome.jp/KEGG.wsdl';
+
+  $results = SOAP::Lite
+               -> service($wsdl)
+               -> list_pathways("eco");
+
+  foreach $path (@{$results}) {
+    print "$path->{entry_id}\t$path->{definition}\n";
+  }
+
+This example colors the boxes corresponding to the E. coli genes b1002
+and b2388 on a Glycolysis pathway of E. coli (path:eco00010).
+
+  #!/usr/bin/env perl
+  
+  use SOAP::Lite;
+  
+  $wsdl = 'http://soap.genome.jp/KEGG.wsdl';
+  
+  $serv = SOAP::Lite -> service($wsdl);
+
+  $genes = SOAP::Data->type(array => ["eco:b1002", "eco:b2388"]);
+
+  $result = $serv -> mark_pathway_by_objects("path:eco00010", $genes);
+
+  print $result;	# URL of the generated image
+
+==== Perl FAQ
+
+As you see in the above example, you always need to convert a Perl's array
+into a SOAP object expicitly in SOAP::Lite by
+
+  SOAP::Data->type(array => [value1, value2, .. ])
+
+when you pass an array as the argument for any KEGG API method.
+
+=== Quick Start with Ruby
+
+If you are using Ruby 1.8.1 or later, you are ready to use KEGG API
+as Ruby already supports SOAP in its standard library.
+
+If your Ruby is 1.6.8 or older, you need to install followings:
+
+  * ((<SOAP4R|URL:http://raa.ruby-lang.org/list.rhtml?name=soap4r>)) 1.5.1 or later
+  * One of the following XML processing library
+    * ((<rexml|URL:http://raa.ruby-lang.org/list.rhtml?name=rexml>))
+    * ((<xmlparser|URL:http://raa.ruby-lang.org/list.rhtml?name=xmlparser>))
+    * ((<xmlscan|URL:http://raa.ruby-lang.org/list.rhtml?name=xmlscan>))
+  * ((<date2|URL:http://raa.ruby-lang.org/list.rhtml?name=date2>))
+  * ((<devel-logger|URL:http://raa.ruby-lang.org/list.rhtml?name=devel-logger>))
+  * ((<uconv|URL:http://raa.ruby-lang.org/list.rhtml?name=uconv>))
+  * ((<http-access2|URL:http://raa.ruby-lang.org/list.rhtml?name=http-access2>))
+
+Here's a sample code for Ruby having the same functionality with Perl's
+first example shown above.
+
+  #!/usr/bin/env ruby
+
+  require 'soap/wsdlDriver'
+
+  wsdl = "http://soap.genome.jp/KEGG.wsdl"
+  serv = SOAP::WSDLDriverFactory.new(wsdl).createDriver
+  serv.generate_explicit_type = true
+  # if uncommented, you can see transactions for debug
+  #serv.wiredump_dev = STDERR
+  
+  start = 1
+  max_results = 5
+
+  top5 = serv.get_best_neighbors_by_gene('eco:b0002', start, max_results)
+  top5.each do |hit|
+    print hit.genes_id1, "\t", hit.genes_id2, "\t", hit.sw_score, "\n"
+  end
+
+You may need to iterate to obtain all the results by increasing start
+and/or max_results.
+
+  #!/usr/bin/env ruby
+  
+  require 'soap/wsdlDriver'
+  
+  wsdl = "http://soap.genome.jp/KEGG.wsdl"
+  serv = SOAP::WSDLDriverFactory.new(wsdl).create_driver
+  serv.generate_explicit_type = true
+
+  start = 1
+  max_results = 100
+  
+  loop do
+    results = serv.get_best_neighbors_by_gene('eco:b0002', start, max_results)
+    break unless results
+    results.each do |hit|
+      print hit.genes_id1, "\t", hit.genes_id2, "\t", hit.sw_score, "\n"
+    end
+    start += max_results
+  end
+
+It is automatically done by using ((<BioRuby|URL:http://bioruby.org/>))
+library, which implements get_all_* methods for this.  BioRuby also
+provides filtering functionality for selecting needed fields from the
+complex data type.
+
+  #!/usr/bin/env ruby
+  
+  require 'bio'
+  
+  serv = Bio::KEGG::API.new
+  
+  results = serv.get_all_best_neighbors_by_gene('eco:b0002')
+
+  results.each do |hit|
+    print hit.genes_id1, "\t", hit.genes_id2, "\t", hit.sw_score, "\n"
+  end
+
+  # Same as above but using filter to select fields
+  fields = [:genes_id1, :genes_id2, :sw_score]
+  results.each do |hit|
+    puts hit.filter(fields).join("\t")
+  end
+
+  # Different filters to pick additional fields for each amino acid sequence
+  fields1 = [:genes_id1, :start_position1, :end_position1, :best_flag_1to2]
+  fields2 = [:genes_id2, :start_position2, :end_position2, :best_flag_2to1]
+  results.each do |hit|
+    print "> score: ", hit.sw_score, ", identity: ", hit.identity, "\n"
+    print "1:\t", hit.filter(fields1).join("\t"), "\n"
+    print "2:\t", hit.filter(fields2).join("\t"), "\n"
+  end
+
+The equivalent for the Perl's second example described above will be
+
+  #!/usr/bin/env ruby
+
+  require 'bio'
+
+  serv = Bio::KEGG::API.new
+
+  list = serv.list_pathways("eco")
+  list.each do |path|
+    print path.entry_id, "\t", path.definition, "\n"
+  end
+
+and equivalent for the last example is as follows.
+
+  #!/usr/bin/env ruby
+  
+  require 'bio'
+
+  serv = Bio::KEGG::API.new
+  
+  genes = ["eco:b1002", "eco:b2388"]
+
+  result = serv.mark_pathway_by_objects("path:eco00010", genes)
+
+  print result		# URL of the generated image
+
+
+=== Quick Start with Python
+
+In the case of Python, you have to install
+
+  * ((<SOAPpy|URL:http://pywebsvcs.sourceforge.net/>))
+
+plus some extra packages required for SOAPpy (
+((<fpconst|URL:http://www.analytics.washington.edu/Zope/projects/fpconst>)),
+((<PyXML|URL:http://pyxml.sourceforge.net/>)) etc.).
+
+Here's a sample code using KEGG API with Python.
+
+  #!/usr/bin/env python
+
+  from SOAPpy import WSDL
+ 
+  wsdl = 'http://soap.genome.jp/KEGG.wsdl'
+  serv = WSDL.Proxy(wsdl)
+
+  results = serv.get_genes_by_pathway('path:eco00020')
+  print results
+
+
+=== Quick Start with Java
+
+In the case of Java, you need to obtain Apache Axis library version
+axis-1_2alpha or newer (axis-1_1 doesn't work properly for KEGG API)
+
+  * ((<Apache Axis|URL:http://ws.apache.org/axis/>))
+
+and put required jar files in an appropriate directory.
+
+For the binary distribution of the Apache axis-1_2alpha release, copy
+the jar files stored under the axis-1_2alpha/lib/ to the directory of
+your choice.
+
+  % cp axis-1_2alpha/lib/*.jar /path/to/lib/
+
+You can use WSDL2Java coming with Apache Axis to generate classes
+needed for the KEGG API automatically.
+
+To generate classes and documents for the KEGG API, download the script
+((<axisfix.pl|URL:http://www.genome.jp/kegg/soap/support/axisfix.pl>))
+and follow the steps below:
+
+  % java -classpath /path/to/lib/axis.jar:/path/to/lib/jaxrpc.jar:/path/to/lib/commons-logging.jar:/path/to/lib/commons-discovery.jar:/path/to/lib/saaj.jar:/path/to/lib/wsdl4j.jar:. org.apache.axis.wsdl.WSDL2Java -p keggapi http://soap.genome.jp/KEGG.wsdl
+  % perl -i axisfix.pl keggapi/KEGGBindingStub.java
+  % javac -classpath /path/to/lib/axis.jar:/path/to/lib/jaxrpc.jar:/path/to/lib/wsdl4j.jar:. keggapi/KEGGLocator.java
+  % jar cvf keggapi.jar keggapi/*
+  % javadoc -classpath /path/to/lib/axis.jar:/path/to/lib/jaxrpc.jar -d keggapi_javadoc keggapi/*.java
+
+This program will do the same job as the Python's example (extended to
+accept a pathway_id as the argument).
+
+  import keggapi.*;
+  
+  class GetGenesByPathway {
+          public static void main(String[] args) throws Exception {
+                  KEGGLocator  locator = new KEGGLocator();
+                  KEGGPortType serv    = locator.getKEGGPort();
+  
+                  String   query   = args[0];
+                  String[] results = serv.get_genes_by_pathway(query);
+  
+                  for (int i = 0; i < results.length; i++) {
+                          System.out.println(results[i]);
+                  }
+          }
+  }
+
+This is another example which uses ArrayOfSSDBRelation data type. 
+
+  import keggapi.*;
+  
+  class GetBestNeighborsByGene {
+          public static void main(String[] args) throws Exception {
+                  KEGGLocator    locator  = new KEGGLocator();
+                  KEGGPortType   serv     = locator.getKEGGPort();
+  
+                  String         query    = args[0];
+                  SSDBRelation[] results  = null;
+  
+                  results = serv.get_best_neighbors_by_gene(query, 1, 50);
+  
+                  for (int i = 0; i < results.length; i++) {
+                          String gene1  = results[i].getGenes_id1();
+                          String gene2  = results[i].getGenes_id2();
+                          int    score  = results[i].getSw_score();
+                          System.out.println(gene1 + "\t" + gene2 + "\t" + score);
+                  }
+          }
+  }
+
+Compile and execute this program (don't forget to include keggapi.jar file
+in your classpath) as follows:
+
+  % javac -classpath /path/to/lib/axis.jar:/path/to/lib/jaxrpc.jar:/path/to/lib/wsdl4j.jar:/path/to/keggapi.jar GetBestNeighborsByGene.java
+
+  % java -classpath /path/to/lib/axis.jar:/path/to/lib/jaxrpc.jar:/path/to/lib/commons-logging.jar:/path/to/lib/commons-discovery.jar:/path/to/lib/saaj.jar:/path/to/lib/wsdl4j.jar:/path/to/keggapi.jar:. GetBestNeighborsByGene eco:b0002
+
+You may wish to set the CLASSPATH environmental variable.
+
+bash/zsh:
+
+  % for i in /path/to/lib/*.jar
+  do
+    CLASSPATH="${CLASSPATH}:${i}"
+  done
+  % export CLASSPATH
+
+tcsh:
+
+  % foreach i ( /path/to/lib/*.jar )
+    setenv CLASSPATH ${CLASSPATH}:${i}
+  end
+
+For the other cases, consult the javadoc pages generated by WSDL2Java.
+
+  * ((<URL:http://www.genome.jp/kegg/soap/doc/keggapi_javadoc/>))
+
+
+== KEGG API Reference
+
+=== WSDL file
+
+Users can use a WSDL file to create a SOAP client driver.  The WSDL file for
+the KEGG API can be found at:
+
+  * ((<URL:http://soap.genome.jp/KEGG.wsdl>))
+
+=== Terminology
+
+  * 'org' is a three-letter organism code used in KEGG.  The list can be
+    found at (see the description of the list_organisms method below):
+
+    * ((<URL:http://www.genome.jp/kegg/catalog/org_list.html>))
+
+  * 'db' is a database name used in GenomeNet service. See the
+    description of the list_databases method below.
+
+  * 'entry_id' is a unique identifier of which format is the combination of
+    the database name and the identifier of an entry joined by a colon sign
+    as 'database:entry' (e.g. 'embl:J00231' means an EMBL entry 'J00231').
+    'entry_id' includes 'genes_id', 'enzyme_id', 'compound_id', 'glycan_id',
+    'reaction_id', 'pathway_id' and 'motif_id' described in below.
+
+  * 'genes_id' is a gene identifier used in KEGG/GENES which consists of
+    'keggorg' and a gene name (e.g. 'eco:b0001' means an E. coli gene 'b0001').
+
+  * 'enzyme_id' is an enzyme identifier consisting of database name 'ec'
+    and an enzyme code used in KEGG/LIGAND (e.g. 'ec:1.1.1.1' means an
+    alcohol dehydrogenase enzyme)
+
+  * 'compound_id' is a compound identifier consisting of database name 'cpd'
+    and a compound number used in KEGG/LIGAND (e.g. 'cpd:C00158' means a
+    citric acid).  Note that some compounds also have 'glycan_id' and
+    both IDs are accepted and converted internally by the corresponding
+    methods.
+
+  * 'glycan_id' is a glycan identifier consisting of database name 'gl'
+    and a glycan number used in KEGG/GLYCAN (e.g. 'gl:G00050' means a
+    Paragloboside).  Note that some glycans also have 'compound_id' and
+    both IDs are accepted and converted internally by the corresponding
+    methods.
+
+  * 'reaction_id' is a reaction identifier consisting of database name 'rn'
+    and a reaction number used in KEGG/REACTION (e.g. 'rn:R00959' is a
+    reaction which catalyze cpd:C00103 into cpd:C00668)
+
+  * 'pathway_id' is a pathway identifier consisting of 'path' and a pathway
+    number used in KEGG/PATHWAY. Pathway numbers prefixed by 'map' specify
+    the reference pathway and pathways prefixed by the 'keggorg' specify
+    pathways specific to the organism (e.g. 'path:map00020' means a reference
+    pathway for the cytrate cycle and 'path:eco00020' means a same pathway of
+    which E. coli genes are marked).
+
+  * 'motif_id' is a motif identifier consisting of motif database names
+    ('ps' for prosite, 'bl' for blocks, 'pr' for prints, 'pd' for prodom,
+    and 'pf' for pfam) and a motif entry name. (e.g. 'pf:DnaJ' means a Pfam
+    database entry 'DnaJ').
+
+  * 'ko_id' is a KO identifier consisting of 'ko' and a ko number used in 
+    KEGG/KO. KO (KEGG Orthology) is an classification of orthologous genes 
+    defined by KEGG (e.g. 'ko:K02598' means a KO group for nitrite transporter
+    NirC genes).
+
+  * 'ko_class_id' is a KO class identifier which is used to classify
+    'ko_id' hierarchically (e.g. '01110' means a 'Carbohydrate Metabolism'
+    class).
+
+    * ((<URL:http://www.genome.jp/dbget-bin/get_htext?KO>))
+
+  * 'start' and 'max_result' are both an integer and used to control the 
+    number of the results returned at once.  Methods having these arguments
+    will return first 'max_result' results starting from 'start'th.
+
+  * 'fg_color_list' is a list of colors for the foreground (corresponding
+    to the texts and borders of the objects on the KEGG pathway map).
+
+  * 'bg_color_list' is a list of colors for the background (corresponding
+    to the inside of the objects on the KEGG pathway map).
+
+=== Returned values
+
+Many of the KEGG API methods will return a set of values in a complex data
+structure as described below.  This section summarizes all kind of these
+data types.  Note that, the retuened values for the empty result will be
+  * an empty array -- for the methods which return ArrayOf'OBJ'
+  * an empty string -- for the methods which return String
+  * -1 -- for the methods which return int
+  * NULL -- for the methods which return any other 'OBJ'
+
++ SSDBRelation
+
+SSDBRelation data type contains the following fields:
+
+  genes_id1         genes_id of the query (string)
+  genes_id2         genes_id of the target (string)
+  sw_score          Smith-Waterman score between genes_id1 and genes_id2 (int)
+  bit_score         bit score between genes_id1 and genes_id2 (float)
+  identity          identity between genes_id1 and genes_id2 (float)
+  overlap           overlap length between genes_id1 and genes_id2 (int)
+  start_position1   start position of the alignment in genes_id1 (int)
+  end_position1     end position of the alignment in genes_id1 (int)
+  start_position2   start position of the alignment in genes_id2 (int)
+  end_position2     end position of the alignment in genes_id2 (int)
+  best_flag_1to2    best flag from genes_id1 to genes_id2 (boolean)
+  best_flag_2to1    best flag from genes_id2 to genes_id1 (boolean)
+  definition1       definition string of the genes_id1 (string)
+  definition2       definition string of the genes_id2 (string)
+  length1           amino acid length of the genes_id1 (int)
+  length2           amino acid length of the genes_id2 (int)
+
+Notice (26 Nov, 2004):
+
+We found a serious bug with the 'best_flag_1to2' and 'best_flag_2to1'
+fields in the SSDBRelation data type.  The methods returning the
+SSDBRelation (and ArrayOfSSDBRelation) data type had returned the
+opposite values of the intended results with the both fields.
+The following methods had been affected by this bug:
+
+# * get_neighbors_by_gene
+  * get_best_neighbors_by_gene
+  * get_reverse_best_neighbors_by_gene
+  * get_paralogs_by_gene
+# * get_similarity_between_genes
+
+This problem is fixed in the version 3.2.
+
++ ArrayOfSSDBRelation
+
+ArrayOfSSDBRelation data type is a list of the SSDBRelation data type.
+
++ MotifResult
+
+MotifResult data type contains the following fields:
+
+  motif_id          motif_id of the motif (string)
+  definition        definition of the motif (string)
+  genes_id          genes_id of the gene containing the motif (string)
+  start_position    start position of the motif match (int)
+  end_position      end position of the motif match (int)
+  score             score of the motif match for TIGRFAM and PROSITE (float)
+  evalue            E-value of the motif match for Pfam (double)
+
+Note: 'score' and/or 'evalue' is set to -1 if the corresponding value is
+not applicable.
+
++ ArrayOfMotifResult
+
+ArrayOfMotifResult data type is a list of the MotifResult data type.
+
++ Definition
+
+Definition data type contains the following fields:
+
+  entry_id          database entry_id (string)
+  definition        definition of the entry (string)
+
++ ArrayOfDefinition
+
+ArrayOfDefinition data type is a list of the Definition data type.
+
++ LinkDBRelation
+
+LinkDBRelation data type contains the following fields:
+
+  entry_id1         entry_id of the starting entry (string)
+  entry_id2         entry_id of the terminal entry (string)
+  type              type of the link as "direct" or "indirect" (string)
+  path              link path information across the databases (string)
+
++ ArrayOfLinkDBRelation
+
+ArrayOfLinkDBRelation data type is a list of the LinkDBRelation data type.
+
+=== Methods
+
+==== Meta information
+
+This section describes the APIs for retrieving the general information 
+concerning latest version of the KEGG database.
+
+--- list_databases
+
+List of database names and its definitions available on the GenomeNet
+is returned.
+
+Return value:
+  ArrayOfDefinition (db, definition)
+
+--- list_organisms
+
+List up the organisms in the KEGG/GENES database. 'org' code and the
+organism's full name is returned in the Definition data type.
+
+Return value:
+  ArrayOfDefinition (org, definition)
+
+--- list_pathways(org)
+
+List up the pathway maps of the given organism in the KEGG/PATHWAY database.
+Passing the string "map" as its argument, this method returns a list of the 
+reference pathways.
+
+Return value:
+  ArrayOfDefinition (pathway_id, definition)
+
+==== DBGET
+
+This section describes the wrapper methods for DBGET system developed
+at the GenomeNet.  For more details on DBGET system, see:
+
+* ((<URL:http://www.genome.jp/dbget/dbget_manual.html>))
+
+--- binfo(string)
+
+Show the version information of the specified database.
+Passing the string "all" as its argument, this method returns the version 
+information of all databases available on the GenomeNet.
+
+Return value:
+  string
+
+Example:
+  # Show the information of the latest GenBank database.
+  binfo("gb")
+
+--- bfind(string)
+
+Wrapper method for bfind command. bfind is used for searching entries by 
+keywords. User need to specify a database from those which are supported 
+by DBGET system before keywords.  Number of keywords given at a time is
+restricted up to 100.
+
+Return value:
+  string
+
+Example:
+  # Returns the IDs and definitions of entries which have definition
+  # including the word 'E-cadherin' and 'human' from GenBank.
+  bfind("gb E-cadherin human")
+
+--- bget(string)
+
+The bget command is used for retrieving database entries specified by a list
+of 'entry_id'.  This method accepts all the bget command line options as
+a string.  Number of entries retrieved at a time is restricted up to 100.
+
+Return value:
+  string
+
+Example:
+  # retrieve two KEGG/GENES entries
+  bget("eco:b0002 hin:tRNA-Cys-1")
+  # retrieve nucleic acid sequences in a FASTA format
+  bget("-f -n n eco:b0002 hin:tRNA-Cys-1")
+  # retrieve amino acid sequence in a FASTA format
+  bget("-f -n a eco:b0002")
+
+--- btit(string)
+
+Wrapper method for btit command. btit is used for retrieving the definitions
+by given database entries.  Number of entries given at a time is restricted
+up to 100.
+
+Return value:
+  string
+
+Example:
+  # Returns the ids and definitions of four GENES entries "hsa:1798",
+  # "mmu:13478", "dme:CG5287-PA" and cel:Y60A3A.14".
+  btit("hsa:1798 mmu:13478 dme:CG5287-PA cel:Y60A3A.14")
+
+==== LinkDB
+
+--- get_linkdb_by_entry(entry_id, db, start, max_results)
+
+Retrieve the database entries linked from the user specified database entry.
+It can also be specified the targeted database.
+
+Return value:
+  ArrayOfLinkDBRelation
+
+Example:
+  # Get the entries of KEGG/PATHWAY database linked from the entry 'eco:b0002'.
+  get_linkdb_by_entry('eco:b0002', 'pathway', 1, 10)
+  get_linkdb_by_entry('eco:b0002', 'pathway', 11, 10)
+
+==== SSDB
+
+This section describes the APIs for SSDB database.  For more details
+on SSDB, see:
+
+  * ((<URL:http://www.genome.jp/kegg/ssdb/>))
+
+#--- get_neighbors_by_gene(genes_id, org, start, max_results)
+#
+#Search homologous genes of the user specified 'genes_id' from specified
+#organism (or from all organisms if 'all' is given as org).
+#
+#Return value:
+#  ArrayOfSSDBRelation
+#
+#Examples:
+#  # This will search all homologous genes of E. coli gene 'b0002'
+#  # in the SSDB and returns the first ten results.
+#  get_neighbors_by_gene('eco:b0002', 'all', 1, 10)
+#  # Next ten results.
+#  get_neighbors_by_gene('eco:b0002', 'all', 11, 10)
+
+--- get_best_best_neighbors_by_gene(genes_id, start, max_results)
+
+Search best-best neighbor of the gene in all organisms.
+
+Return value:
+  ArrayOfSSDBRelation
+
+Example:
+  # List up best-best neighbors of 'eco:b0002'.
+  get_best_best_neighbors_by_gene('eco:b0002', 1, 10)
+  get_best_best_neighbors_by_gene('eco:b0002', 11, 10)
+
+--- get_best_neighbors_by_gene(genes_id, start, max_results)
+
+Search best neighbors in all organism.
+
+Return value:
+  ArrayOfSSDBRelation
+
+Example:
+  # List up best neighbors of 'eco:b0002'.
+  get_best_neighbors_by_gene('eco:b0002', 1, 10)
+  get_best_neighbors_by_gene('eco:b0002', 11, 10)
+
+--- get_reverse_best_neighbors_by_gene(genes_id, start, max_results)
+
+Search reverse best neighbors in all organisms.
+
+Return value:
+  ArrayOfSSDBRelation
+
+Example:
+  # List up reverse best neighbors of 'eco:b0002'.
+  get_reverse_best_neighbors_by_gene('eco:b0002', 1, 10)
+  get_reverse_best_neighbors_by_gene('eco:b0002', 11, 10)
+
+--- get_paralogs_by_gene(genes_id, start, max_results)
+
+Search paralogous genes of the given gene in the same organism.
+
+Return value:
+  ArrayOfSSDBRelation
+
+Example:
+  # List up paralogous genes of 'eco:b0002'.
+  get_paralogs_by_gene('eco:b0002', 1, 10)
+  get_paralogs_by_gene('eco:b0002', 11, 10)
+
+#--- get_similarity_between_genes(genes_id1, genes_id2)
+#
+#Returns data containing Smith-Waterman score and alignment positions
+#between the two genes.
+#
+#Return value:
+#  SSDBRelation
+#
+#Example:
+#  # Returns a 'sw_score' between two E. coli genes 'b0002' and 'b3940'
+#  get_similarity_between_genes('eco:b0002', 'eco:b3940')
+
+==== Motif
+
+--- get_motifs_by_gene(genes_id, db)
+
+Search motifs in the specified gene. As for 'db', 
+user can specify one of the four database; Pfam, TIGRFAM, PROSITE pattern,
+PROSITE profile as 'pfam', 'tfam', 'pspt', 'pspf', respectively.
+You can also use 'all' to specify all of the four databases above.
+
+Return value:
+  ArrayOfMotifResult
+
+Example:
+  # Returns the all pfam motifs in the E. coli gene 'b0002'
+  get_motifs_by_gene('eco:b0002', 'pfam')
+
+--- get_genes_by_motifs(motif_id_list, start, max_results)
+
+Search all genes which contains all of the specified motifs.
+
+Return value:
+  ArrayOfDefinition (genes_id, definition)
+
+Example:
+  # Returns all genes which have Pfam 'DnaJ' and Prosite 'DNAJ_2' motifs.
+  list = ['pf:DnaJ', 'ps:DNAJ_2']
+  get_genes_by_motifs(list, 1, 10)
+  get_genes_by_motifs(list, 11, 10)
+
+
+==== KO, OC, PC
+
+--- get_ko_by_gene(genes_id)
+
+Search all KOs to which given genes_id belongs.
+
+Return value:
+  ArrayOfstring (ko_id)
+
+Example:
+  # Returns ko_ids to which GENES entry 'eco:b0002' belongs.
+  get_ko_by_gene('eco:b0002')
+
+#--- get_ko_members(ko_id)
+#
+#Returns all genes assigned to the given KO entry.
+#
+#Return value:
+#  ArrayOfstring (genes_id)
+#
+#Example
+#  # Returns genes_ids those which belong to KO entry 'ko:K02598'.
+#  get_ko_members('ko:K02598')
+
+--- get_ko_by_ko_class(ko_class_id)
+
+Return all KOs which belong to the given ko_class_id.
+
+Return value:
+  ArrayOfDefinition (ko_id, definition)
+
+Example:
+  # Returns ko_ids which belong to the KO class '01196'.
+  get_ko_by_ko_class('01196')
+
+--- get_genes_by_ko_class(ko_class_id, org, start, max_results)
+
+Retrieve all genes of the specified organism which are classified
+under the given ko_class_id.
+
+Return value:
+  ArrayOfDefinition (genes_id, definition)
+
+Example:
+  # Returns first 100 human genes which belong to the KO class '00930'
+  get_genes_by_ko_class('00903', 'hsa' , 1, 100)
+
+--- get_genes_by_ko(ko_id, org)
+
+Retrieve all genes of the specified organism which belong to the
+given ko_id.
+
+Return value:
+  ArrayOfDefinition (genes_id, definition)
+
+Example
+  # Returns E.coli genes which belong to the KO 'K00001'
+  get_genes_by_ko('ko:K00001', 'eco')
+
+  # Returns genes of all organisms which are assigned to the KO 'K00010'
+  get_genes_by_ko('ko:K00010', 'all')
+
+--- get_oc_members_by_gene(genes_id, start, max_results)
+
+Search all members of the same OC (KEGG Ortholog Cluster) to which given
+genes_id belongs.
+
+Return value:
+  ArrayOfstring (genes_id)
+
+Example
+  # Returns genes belonging to the same OC with eco:b0002 gene.
+  get_oc_members_by_gene('eco:b0002', 1, 10)
+  get_oc_members_by_gene('eco:b0002', 11, 10)
+
+--- get_pc_members_by_gene(genes_id, start, max_results)
+
+Search all members of the same PC (KEGG Paralog Cluster) to which given
+genes_id belongs.
+
+Return value:
+  ArrayOfstring (genes_id)
+
+Example
+  # Returns genes belonging to the same PC with eco:b0002 gene.
+  get_pc_members_by_gene('eco:b0002', 1, 10)
+  get_pc_members_by_gene('eco:b0002', 11, 10)
+
+
+==== PATHWAY
+
+This section describes the APIs for PATHWAY database.  For more details
+on PATHWAY database, see:
+
+  * ((<URL:http://www.genome.jp/kegg/kegg2.html#pathway>))
+
++ Coloring pathways
+
+--- mark_pathway_by_objects(pathway_id, object_id_list)
+
+Mark the given objects on the given pathway map and return the URL of the
+generated image.
+
+Return value:
+  string (URL)
+
+Example:
+  # Returns the URL of the generated image for the given map 'path:eco00260'
+  # with objects corresponding to 'eco:b0002' and 'cpd:C00263' colored in red.
+  obj_list = ['eco:b0002', 'cpd:C00263']
+  mark_pathway_by_objects('path:eco00260', obj_list)
+
+--- color_pathway_by_objects(pathway_id, object_id_list, fg_color_list, bg_color_list)
+
+Color the given objects on the pathway map with the specified colors 
+and return the URL of the colored image.  In the KEGG pathway maps,
+a gene or enzyme is represented by a rectangle and a compound is
+shown as a small circle.  'fg_color_list' is used for specifying the
+color of text and border of the given objects and 'bg_color_list' is
+used for its background area.  The order of colors in these lists
+correspond with the order of objects in the 'object_id_list' list.
+
+Return value:
+  string (URL)
+
+Example:
+  # Returns the URL for the given pathway 'path:eco00260' with genes
+  # 'eco:b0514' colored in red with yellow background and
+  # 'eco:b2913' colored in green with yellow background.
+  obj_list = ['eco:b0514', 'eco:b2913']
+  fg_list  = ['#ff0000', '#00ff00']
+  bg_list  = ['#ffff00', 'yellow']
+  color_pathway_by_objects('path:eco00260', obj_list, fg_list, bg_list)
+
+--- get_html_of_marked_pathway_by_objects(pathway_id, object_id_list)
+
+HTML version of the 'mark_pathway_by_objects' method.
+Mark the given objects on the given pathway map and return the URL of the
+HTML with the generated image as a clickable map.
+
+Return value:
+  string (URL)
+
+Example:
+  # Returns the URL of the HTML which can be passed to the web browser
+  # as a clickable map of the generated image of the given pathway
+  # 'path:eco00970' with three objects corresponding to 'eco:b4258',
+  # 'cpd:C00135' and 'ko:K01881' colored in red.
+  obj_list = ['eco:b4258', 'cpd:C00135', 'ko:K01881']
+  get_html_of_marked_pathway_by_objects('path:eco00970', obj_list)
+
+--- get_html_of_colored_pathway_by_objects(pathway_id, object_id_list, fg_color_list, bg_color_list)
+
+HTML version of the 'color_pathway_by_object' method.
+Color the given objects on the pathway map with the specified colors 
+and return the URL of the HTML containing the colored image as a
+clickable map.
+
+Return value:
+  string (URL)
+
+Example:
+  # Returns the URL of the HTML which can be passed to the web browser
+  # as a clickable map of coloerd image of the given pathway 'path:eco00970'
+  # with a gene 'eco:b4258' colored in gray/red, a compound 'cpd:C00135'
+  # coloerd in green/yellow and a KO 'ko:K01881' colored in blue/orange.
+  obj_list = ['eco:b4258', 'cpd:C00135', 'ko:K01881']
+  fg_list  = ['gray', '#00ff00', 'blue']
+  bg_list  = ['#ff0000', 'yellow', 'orange']
+  get_html_of_colored_pathway_by_objects('path:eco00970', obj_list, fg_list, bg_list)
+
+
++ Objects on the pathway
+
+--- get_genes_by_pathway(pathway_id)
+
+Search all genes on the specified pathway.  Organism name is given by
+the name of the pathway map.
+
+Return value:
+  ArrayOfstring (genes_id)
+
+Example:
+  # Returns all E. coli genes on the pathway map '00020'.
+  get_genes_by_pathway('path:eco00020')
+
+--- get_enzymes_by_pathway(pathway_id)
+
+Search all enzymes on the specified pathway.
+
+Return value:
+  ArrayOfstring (enzyme_id)
+
+Example:
+  # Returns all E. coli enzymes on the pathway map '00020'.
+  get_enzymes_by_pathway('path:eco00020')
+
+--- get_compounds_by_pathway(pathway_id)
+
+Search all compounds on the specified pathway.
+
+Return value:
+  ArrayOfstring (compound_id)
+
+Example:
+  # Returns all E. coli compounds on the pathway map '00020'.
+  get_compounds_by_pathway('path:eco00020')
+
+--- get_glycans_by_pathway(pathway_id)
+
+Search all glycans on the specified pathway.
+
+Return value:
+  ArrayOfstring (glycan_id)
+
+Example
+  # Returns all E. coli glycans on the pathway map '00510'
+  get_glycans_by_pathway('path:eco00510')
+
+--- get_reactions_by_pathway(pathway_id)
+
+Retrieve all reactions on the specified pathway.
+
+Return value:
+  ArrayOfstring (reaction_id)
+
+Example:
+  # Returns all E. coli reactions on the pathway map '00260'
+  get_reactions_by_pathway('path:eco00260')
+
+--- get_kos_by_pathway(pathway_id)
+
+Retrieve all KOs on the specified pathway.
+
+Return value:
+  ArrayOfstring (ko_id)
+
+Example:
+  # Returns all ko_ids on the pathway map 'path:hsa00010'
+  get_kos_by_pathway('path:hsa00010')
+
+
++ Pathways by objects
+
+--- get_pathways_by_genes(genes_id_list)
+
+Search all pathways which include all the given genes.  How to pass the
+list of genes_id will depend on the language specific implementations.
+
+Return value:
+  ArrayOfstring (pathway_id)
+
+Example:
+  # Returns all pathways including E. coli genes 'b0077' and 'b0078'
+  get_pathways_by_genes(['eco:b0077' , 'eco:b0078'])
+
+--- get_pathways_by_enzymes(enzyme_id_list)
+
+Search all pathways which include all the given enzymes.
+
+Return value:
+  ArrayOfstring (pathway_id)
+
+Example:
+  # Returns all pathways including an enzyme '1.3.99.1'
+  get_pathways_by_enzymes(['ec:1.3.99.1'])
+
+--- get_pathways_by_compounds(compound_id_list)
+
+Search all pathways which include all the given compounds.
+
+Return value:
+  ArrayOfstring (pathway_id)
+
+Example:
+  # Returns all pathways including compounds 'C00033' and 'C00158'
+  get_pathways_by_compounds(['cpd:C00033', 'cpd:C00158'])
+
+--- get_pathways_by_glycans(glycan_id_list)
+
+Search all pathways which include all the given glycans.
+ 
+Return value:
+  ArrayOfstring (pathway_id)
+
+Example
+  # Returns all pathways including glycans 'G00009' and 'G00011'
+  get_pathways_by_glycans(['gl:G00009', 'gl:G00011'])
+
+--- get_pathways_by_reactions(reaction_id_list)
+
+Retrieve all pathways which include all the given reaction_ids.
+
+Return value:
+  ArrayOfstring (pathway_id)
+
+Example:
+  # Returns all pathways including reactions 'rn:R00959', 'rn:R02740',
+  # 'rn:R00960' and 'rn:R01786'
+  get_pathways_by_reactions(['rn:R00959', 'rn:R02740', 'rn:R00960', 'rn:R01786'])
+
+--- get_pathways_by_kos(ko_id_list, org)
+
+Retrieve all pathways of the organisms which include all the given KO IDs.
+
+Return value:
+  ArrayOfstring (pathway_id)
+
+Example:
+  # Returns all human pathways including 'ko:K00016' and 'ko:K00382'
+  get_pathways_by_kos(['ko:K00016', 'ko:K00382'], 'hsa')
+
+  # Returns pathways of all organisms including 'ko:K00016' and 'ko:K00382'
+  get_pathways_by_kos(['ko:K00016', 'ko:K00382'], 'all')
+
+
++ Relation among pathways
+
+--- get_linked_pathways(pathway_id)
+
+Retrieve all pathways which are linked from a given pathway_id.
+
+Return value:
+  ArrayOfstring (pathway_id)
+
+Example:
+  # Returns IDs of PATHWAY entries linked from 'path:eco00620'.
+  get_linked_pathways('path:eco00620')
+
+
++ Relation among genes and enzymes
+
+--- get_genes_by_enzyme(enzyme_id, org)
+
+Retrieve all genes of the given organism.
+
+Return value:
+  ArrayOfstring (genes_id)
+
+Example:
+  # Returns all the GENES entry IDs in E.coli genome which are assigned 
+  # EC number ec:1.2.1.1
+  get_genes_by_enzyme('ec:1.2.1.1', 'eco')
+
+--- get_enzymes_by_gene(genes_id)
+
+Retrieve all the EC numbers which are assigned to the given gene.
+
+Return value:
+  ArrayOfstring (enzyme_id)
+
+Example:
+  # Returns the EC numbers which are assigned to E.coli genes b0002
+  get_enzymes_by_gene('eco:b0002')
+
+
++ Relation among enzymes, compounds and reactions
+
+--- get_enzymes_by_compound(compound_id)
+
+Retrieve all enzymes which have a link to the given compound_id.
+
+Return value:
+  ArrayOfstring (enzyme_id)
+
+Example:
+  # Returns the ENZYME entry IDs which have a link to the COMPOUND entry,
+  # 'cpd:C00345'
+  get_enzymes_by_compound('cpd:C00345')
+
+--- get_enzymes_by_glycan(glycan_id)
+
+Retrieve all enzymes which have a link to the given glycan_id.
+
+Return value:
+  ArrayOfstring (enzyme_id)
+
+Example
+  # Returns the ENZYME entry IDs which have a link to the GLYCAN entry,
+  # 'gl:G00001'
+  get_enzymes_by_glycan('gl:G00001')
+
+--- get_enzymes_by_reaction(reaction_id)
+
+Retrieve all enzymes which have a link to the given reaction_id.
+
+Return value:
+  ArrayOfstring (enzyme_id)
+
+Example:
+  # Returns the ENZYME entry IDs which have a link to the REACTION entry, 
+  # 'rn:R00100'.
+  get_enzymes_by_reaction('rn:R00100')
+
+--- get_compounds_by_enzyme(enzyme_id)
+
+Retrieve all compounds which have a link to the given enzyme_id.
+
+Return value:
+  ArrayOfstring (compound_id)
+
+Example:
+  # Returns the COMPOUND entry IDs which have a link to the ENZYME entry, 
+  # 'ec:2.7.1.12'.
+  get_compounds_by_enzyme('ec:2.7.1.12')
+ 
+--- get_compounds_by_reaction(reaction_id)
+
+Retrieve all compounds which have a link to the given reaction_id.
+
+Return value:
+  ArrayOfstring (compound_id)
+
+Example:
+  # Returns the COMPOUND entry IDs which have a link to the REACTION entry, 
+  # 'rn:R00100'
+  get_compounds_by_reaction('rn:R00100')
+
+--- get_glycans_by_enzyme(enzyme_id)
+
+Retrieve all glycans which have a link to the given enzyme_id.
+
+Return value:
+  ArrayOfstring (glycan_id)
+
+Example
+  # Returns the GLYCAN entry IDs which have a link to the ENZYME entry,
+  # 'ec:2.4.1.141'
+  get_glycans_by_enzyme('ec:2.4.1.141')
+
+--- get_glycans_by_reaction(reaction_id)
+
+Retrieve all glycans which have a link to the given reaction_id.
+
+Return value:
+  ArrayOfstring (glycan_id)
+
+Example
+  # Returns the GLYCAN entry IDs which have a link to the REACTION entry,
+  # 'rn:R06164'
+  get_glycans_by_reaction('rn:R06164')
+
+--- get_reactions_by_enzyme(enzyme_id)
+
+Retrieve all reactions which have a link to the given enzyme_id.
+
+Return value:
+  ArrayOfstring (reaction_id)
+
+Example:
+  # Returns the REACTION entry IDs which have a link to the ENZYME entry,
+  # 'ec:2.7.1.12'
+  get_reactions_by_enzyme('ec:2.7.1.12')
+
+--- get_reactions_by_compound(compound_id)
+
+Retrieve all reactions which have a link to the given compound_id.
+
+Return value:
+  ArrayOfstring (reaction_id)
+
+Example:
+  # Returns the REACTION entry IDs which have a link to the COMPOUND entry,
+  # 'cpd:C00199'
+  get_reactions_by_compound('cpd:C00199')
+
+--- get_reactions_by_glycan(glycan_id)
+
+Retrieve all reactions which have a link to the given glycan_id.
+
+Return value:
+  ArrayOfstring (reaction_id)
+
+Example
+  # Returns the REACTION entry IDs which have a link to the GLYCAN entry,
+  # 'gl:G00001'
+  get_reactions_by_glycan('gl:G00001')
+
+
+==== GENES
+
+This section describes the APIs for GENES database. For more details
+on GENES database, see:
+
+  * ((<URL:http://www.genome.jp/kegg/kegg2.html#genes>))
+
+--- get_genes_by_organism(org, start, max_results)
+
+Retrieve all genes of the specified organism.
+
+Return value:
+  ArrayOfstring (genes_id)
+
+Example:
+  # Retrive hundred H. influenzae genes at once.
+  get_genes_by_organism('hin', 1, 100)
+  get_genes_by_organism('hin', 101, 100)
+
+
+==== GENOME
+
+This section describes the APIs for GENOME database. For more details
+on GENOME database, see:
+
+  * ((<URL:http://www.genome.jp/kegg/kegg2.html#genome>))
+
+--- get_number_of_genes_by_organism(org)
+
+Get the number of genes coded in the specified organism's genome. 
+
+Return value:
+  int
+
+Example:
+  # Get the number of the genes on the E.coli genome.
+  get_number_of_genes_by_organism('eco')
+
+
+==== LIGAND
+
+This section describes the APIs for LIGAND database.
+
+--- convert_mol_to_kcf(mol_text)
+
+Convert a MOL format into the KCF format.
+
+Return value:
+  string
+
+Example:
+  convert_mol_to_kcf(mol_str)
+
+
+== Notes
+
+Last updated: May 31, 2005
+
+=end
+