bio 1.4.3.0001 → 1.5.0
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- checksums.yaml +7 -0
- data/.travis.yml +39 -33
- data/BSDL +22 -0
- data/COPYING +2 -2
- data/COPYING.ja +36 -36
- data/ChangeLog +2404 -1025
- data/KNOWN_ISSUES.rdoc +15 -55
- data/README.rdoc +17 -23
- data/RELEASE_NOTES.rdoc +246 -183
- data/Rakefile +3 -2
- data/bin/br_biofetch.rb +29 -5
- data/bioruby.gemspec +15 -32
- data/bioruby.gemspec.erb +10 -20
- data/doc/ChangeLog-1.4.3 +1478 -0
- data/doc/RELEASE_NOTES-1.4.3.rdoc +204 -0
- data/doc/Tutorial.rd +0 -6
- data/doc/Tutorial.rd.html +7 -12
- data/doc/Tutorial.rd.ja +960 -1064
- data/doc/Tutorial.rd.ja.html +977 -1067
- data/gemfiles/Gemfile.travis-jruby1.8 +2 -1
- data/gemfiles/Gemfile.travis-jruby1.9 +2 -4
- data/gemfiles/Gemfile.travis-rbx +13 -0
- data/gemfiles/Gemfile.travis-ruby1.8 +2 -1
- data/gemfiles/Gemfile.travis-ruby1.9 +2 -4
- data/gemfiles/Gemfile.travis-ruby2.2 +9 -0
- data/lib/bio.rb +10 -43
- data/lib/bio/alignment.rb +8 -14
- data/lib/bio/appl/blast.rb +1 -2
- data/lib/bio/appl/blast/format0.rb +18 -7
- data/lib/bio/appl/blast/remote.rb +0 -9
- data/lib/bio/appl/blast/report.rb +1 -1
- data/lib/bio/appl/clustalw/report.rb +3 -1
- data/lib/bio/appl/genscan/report.rb +1 -2
- data/lib/bio/appl/iprscan/report.rb +1 -2
- data/lib/bio/appl/meme/mast.rb +4 -4
- data/lib/bio/appl/meme/mast/report.rb +1 -1
- data/lib/bio/appl/paml/codeml.rb +2 -2
- data/lib/bio/appl/paml/codeml/report.rb +1 -0
- data/lib/bio/appl/paml/common.rb +1 -1
- data/lib/bio/appl/sosui/report.rb +1 -2
- data/lib/bio/command.rb +62 -2
- data/lib/bio/data/aa.rb +13 -31
- data/lib/bio/data/codontable.rb +1 -2
- data/lib/bio/db/biosql/biosql_to_biosequence.rb +1 -0
- data/lib/bio/db/biosql/sequence.rb +1 -1
- data/lib/bio/db/embl/common.rb +1 -1
- data/lib/bio/db/embl/embl.rb +5 -4
- data/lib/bio/db/embl/format_embl.rb +3 -3
- data/lib/bio/db/embl/sptr.rb +9 -1444
- data/lib/bio/db/embl/swissprot.rb +12 -29
- data/lib/bio/db/embl/trembl.rb +13 -30
- data/lib/bio/db/embl/uniprot.rb +12 -29
- data/lib/bio/db/embl/uniprotkb.rb +1455 -0
- data/lib/bio/db/fasta.rb +17 -0
- data/lib/bio/db/fasta/defline.rb +1 -3
- data/lib/bio/db/fastq.rb +1 -1
- data/lib/bio/db/genbank/ddbj.rb +9 -5
- data/lib/bio/db/genbank/refseq.rb +11 -3
- data/lib/bio/db/gff.rb +3 -4
- data/lib/bio/db/go.rb +5 -6
- data/lib/bio/db/kegg/module.rb +4 -5
- data/lib/bio/db/kegg/pathway.rb +4 -5
- data/lib/bio/db/kegg/reaction.rb +1 -1
- data/lib/bio/db/nexus.rb +3 -2
- data/lib/bio/db/pdb/pdb.rb +2 -2
- data/lib/bio/db/phyloxml/phyloxml_elements.rb +82 -59
- data/lib/bio/db/phyloxml/phyloxml_parser.rb +2 -2
- data/lib/bio/db/phyloxml/phyloxml_writer.rb +1 -2
- data/lib/bio/db/sanger_chromatogram/chromatogram.rb +1 -2
- data/lib/bio/db/transfac.rb +1 -1
- data/lib/bio/io/das.rb +40 -41
- data/lib/bio/io/fastacmd.rb +0 -16
- data/lib/bio/io/fetch.rb +111 -55
- data/lib/bio/io/flatfile/buffer.rb +4 -5
- data/lib/bio/io/hinv.rb +2 -3
- data/lib/bio/io/ncbirest.rb +43 -6
- data/lib/bio/io/pubmed.rb +76 -81
- data/lib/bio/io/togows.rb +33 -10
- data/lib/bio/map.rb +1 -1
- data/lib/bio/pathway.rb +1 -1
- data/lib/bio/sequence/compat.rb +1 -1
- data/lib/bio/sequence/na.rb +63 -12
- data/lib/bio/shell.rb +0 -2
- data/lib/bio/shell/core.rb +5 -6
- data/lib/bio/shell/interface.rb +3 -4
- data/lib/bio/shell/irb.rb +1 -2
- data/lib/bio/shell/plugin/entry.rb +2 -3
- data/lib/bio/shell/plugin/seq.rb +7 -6
- data/lib/bio/shell/setup.rb +1 -2
- data/lib/bio/tree.rb +2 -2
- data/lib/bio/util/contingency_table.rb +0 -2
- data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +2 -2
- data/lib/bio/util/sirna.rb +76 -16
- data/lib/bio/version.rb +8 -9
- data/sample/benchmark_clustalw_report.rb +47 -0
- data/sample/biofetch.rb +248 -151
- data/setup.rb +6 -7
- data/test/data/clustalw/example1-seqnos.aln +58 -0
- data/test/network/bio/appl/blast/test_remote.rb +1 -15
- data/test/network/bio/appl/test_blast.rb +0 -12
- data/test/network/bio/io/test_pubmed.rb +49 -0
- data/test/network/bio/io/test_togows.rb +0 -1
- data/test/network/bio/test_command.rb +65 -2
- data/test/unit/bio/appl/bl2seq/test_report.rb +0 -1
- data/test/unit/bio/appl/blast/test_report.rb +110 -48
- data/test/unit/bio/appl/clustalw/test_report.rb +67 -51
- data/test/unit/bio/appl/sim4/test_report.rb +46 -17
- data/test/unit/bio/appl/test_blast.rb +2 -2
- data/test/unit/bio/db/embl/test_embl.rb +0 -1
- data/test/unit/bio/db/embl/test_embl_rel89.rb +0 -1
- data/test/unit/bio/db/embl/{test_sptr.rb → test_uniprotkb.rb} +111 -115
- data/test/unit/bio/db/embl/{test_uniprot_new_part.rb → test_uniprotkb_new_part.rb} +11 -11
- data/test/unit/bio/db/genbank/test_genbank.rb +10 -4
- data/test/unit/bio/db/pdb/test_pdb.rb +14 -8
- data/test/unit/bio/db/test_fasta.rb +41 -1
- data/test/unit/bio/db/test_fastq.rb +14 -4
- data/test/unit/bio/db/test_gff.rb +2 -2
- data/test/unit/bio/db/test_phyloxml.rb +30 -30
- data/test/unit/bio/db/test_phyloxml_writer.rb +2 -2
- data/test/unit/bio/io/flatfile/test_autodetection.rb +1 -2
- data/test/unit/bio/io/flatfile/test_buffer.rb +7 -1
- data/test/unit/bio/io/flatfile/test_splitter.rb +1 -1
- data/test/unit/bio/io/test_togows.rb +3 -2
- data/test/unit/bio/sequence/test_dblink.rb +1 -1
- data/test/unit/bio/sequence/test_na.rb +3 -1
- data/test/unit/bio/test_alignment.rb +1 -2
- data/test/unit/bio/test_command.rb +5 -4
- data/test/unit/bio/test_db.rb +4 -2
- data/test/unit/bio/test_pathway.rb +25 -10
- data/test/unit/bio/util/test_sirna.rb +22 -22
- metadata +656 -1430
- data/doc/KEGG_API.rd +0 -1843
- data/doc/KEGG_API.rd.ja +0 -1834
- data/extconf.rb +0 -2
- data/lib/bio/appl/blast/ddbj.rb +0 -131
- data/lib/bio/db/kegg/taxonomy.rb +0 -280
- data/lib/bio/io/dbget.rb +0 -194
- data/lib/bio/io/ddbjrest.rb +0 -344
- data/lib/bio/io/ddbjxml.rb +0 -458
- data/lib/bio/io/ebisoap.rb +0 -158
- data/lib/bio/io/ensembl.rb +0 -229
- data/lib/bio/io/higet.rb +0 -73
- data/lib/bio/io/keggapi.rb +0 -363
- data/lib/bio/io/ncbisoap.rb +0 -156
- data/lib/bio/io/soapwsdl.rb +0 -119
- data/lib/bio/shell/plugin/keggapi.rb +0 -181
- data/lib/bio/shell/plugin/soap.rb +0 -87
- data/sample/dbget +0 -37
- data/sample/demo_ddbjxml.rb +0 -212
- data/sample/demo_kegg_taxonomy.rb +0 -92
- data/sample/demo_keggapi.rb +0 -502
- data/sample/psortplot_html.rb +0 -214
- data/test/network/bio/io/test_ddbjrest.rb +0 -47
- data/test/network/bio/io/test_ensembl.rb +0 -230
- data/test/network/bio/io/test_soapwsdl.rb +0 -53
- data/test/unit/bio/io/test_ddbjxml.rb +0 -81
- data/test/unit/bio/io/test_ensembl.rb +0 -111
- data/test/unit/bio/io/test_soapwsdl.rb +0 -33
data/doc/KEGG_API.rd.ja
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$Id: KEGG_API.rd.ja,v 1.11 2006/12/27 13:40:45 k Exp $
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Copyright (C) 2003-2006 Toshiaki Katayama <k@bioruby.org>
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= KEGG API
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KEGG API �ϥץ������ʤɤ��� KEGG �����Ѥ��뤿��Υ����֥����ӥ��Ǥ���
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��Ⱦ�Ǥϡ�KEGG �ǡ����١�������������������긡�������ꤹ�뤿���
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KEGG API ��Ȥ���ˡ���������ޤ�����Ⱦ�Υ�ե���� KEGG API ������ǽ��
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���⤷�ޤ�����Ȥ��Ƽ�� Ruby �����ȤäƲ��⤷�ޤ�����SOAP �� WSDL ��
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�������ȤΤǤ�������Perl, Python, Java �ʤɡˤǤ���д�ñ�� KEGG API ��
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���Ѥ��뤳�Ȥ��Ǥ��ޤ���
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== �ܼ�
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* ((<KEGG API �λȤ���>))
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* ((<KEGG API ��ե����>))
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* ((<WSDL �ե�����>))
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* ((<����ͤΥǡ�����>))
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* ((<LinkDBRelation ��>)), ((<ArrayOfLinkDBRelation ��>))
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* ((<PathwayElement ��>)), ((<ArrayOfPathwayElement ��>))
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* ((<PathwayElementRelation ��>)), ((<ArrayOfPathwayElementRelation ��>))
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* ((<��åɰ���>))
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�����ˤ������Ȥ����ꡢXML �����ˤϴ�Ϣ���Ѥ�·�äƤ��뤳�Ȥ�ʣ���ʥǡ���
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�����֥����ӥ��Ǥ� XML ��Ϣ���Ѥ���Ǥ� SOAP �� WSDL ��Ȥ����Ȥ�¿���ʤä�
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���ޤ���SOAP �ϥ��饤����Ȥȥ����Ф����Ȥꤹ���å�������ɽ����ˡ��
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ɸ�ಽ������Τǡ������� Simple Object Access Method ��ά�Ȥ���Ƥ��ޤ���
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(���� Service Oriented Access Protocol �Ȥ������Ȥ⤢��褦�Ǥ�)��
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WSDL �� SOAP �˴�Ť������ӥ���ԥ塼������ñ�����ѤǤ���褦�ˤ���
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����Τ�Τǡ�Web Service Description Language ��ά�ȤʤäƤ��ޤ���
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KEGG API �Ϥ����ε��Ѥ�Ȥäơ���ʬ�ζ�̣��������Ҥ�ѥ��������ʤɤ�
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�����ͳ�˸�����������Ϥ��Ѥ����ꤹ�뤿��μ��ʤ����ޤ����桼����
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KEGG ��¿���ε�ǽ�����֥ڡ�����å���������˼�ʬ�Υץ�������
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�椫�鼡���ȼ¹Ԥ��뤳�Ȥ��Ǥ���褦�ˤʤ�ޤ���
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KEGG API �˴ؤ���ǿ��ξ���ϰʲ��� URL �������뤳�Ȥ��Ǥ��ޤ���
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154
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|
155
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* ((<URL:http://www.genome.jp/kegg/soap/>))
|
156
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-
|
157
|
-
== KEGG API �λȤ���
|
158
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-
|
159
|
-
�ʲ��Ǥ� Ruby, Perl, Python, Java �γƸ���ˤ�� KEGG API �δ�ñ�ʻȤ�����
|
160
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�Ҳ𤷤ޤ����Ƹ���� SOAP �� WSDL ����饤�֥����ɲå��ȡ��뤹��
|
161
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ɬ�פ�����ޤ���
|
162
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|
163
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=== Ruby ��
|
164
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-
|
165
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Ruby 1.8.1 �ʹߤǤϡ�ɸ��� SOAP ��Ȥ������Ǥ��ޤ��Τ��ɲå��ȡ�
|
166
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���ɬ�פ���ޤ���
|
167
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-
|
168
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Ruby 1.8.0 �Ǥ�
|
169
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((<SOAP4R|URL:http://raa.ruby-lang.org/list.rhtml?name=soap4r>)),
|
170
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((<devel-logger|URL:http://raa.ruby-lang.org/list.rhtml?name=devel-logger>)),
|
171
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((<http-access2|URL:http://raa.ruby-lang.org/list.rhtml?name=http-access2>))
|
172
|
-
�ʤɤΥ饤�֥��ȡ��뤹��ɬ�פ�����ޤ���
|
173
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-
|
174
|
-
Ruby 1.6.8 �ξ��Ϥ���� SOAP4R ��ɬ�פȤ���¾�Υ饤�֥�� (date2, uconv,
|
175
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XML �Υѡ����ʤ�) �⥤�ȡ��뤹��ɬ�פ�����ޤ��Τǡ����餫���� SOAP4R
|
176
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�Υɥ�����Ȥ˽��ä�����Ƥ����ޤ���
|
177
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-
|
178
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�ʲ��Υ���ץ륳���ɤϡ���IJ�ݤ� b0002 �����ҤȺǤ���Ʊ���ι⤤������
|
179
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��Smith-Waterman �������ι⤤��� 5 �ĸ�������ɽ������ץ������Ǥ���
|
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|
181
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#!/usr/bin/env ruby
|
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-
|
183
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require 'soap/wsdlDriver'
|
184
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-
|
185
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wsdl = "http://soap.genome.jp/KEGG.wsdl"
|
186
|
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serv = SOAP::WSDLDriverFactory.new(wsdl).create_rpc_driver
|
187
|
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serv.generate_explicit_type = true # SOAP �� Ruby �η��Ѵ���ͭ���ˤ���
|
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-
|
189
|
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offset = 1
|
190
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limit = 5
|
191
|
-
|
192
|
-
top5 = serv.get_best_neighbors_by_gene('eco:b0002', offset, limit)
|
193
|
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top5.each do |hit|
|
194
|
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print hit.genes_id1, "\t", hit.genes_id2, "\t", hit.sw_score, "\n"
|
195
|
-
end
|
196
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-
|
197
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�ץ���������� 'get_best_neighbors_by_gene' �ϡ�KEGG �� SSDB �ǡ���
|
198
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�١�����Ȥä� KEGG �� GENES �˴ޤޤ�Ƥ������ʪ����椫��Ǥ���Ʊ��
|
199
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�ι⤤�����Ҥ�õ���Ƥ��� API �Ǥ�����̤ϼ��Τ褦��ɽ������ޤ���
|
200
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-
|
201
|
-
eco:b0002 eco:b0002 5283
|
202
|
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eco:b0002 ecj:JW0001 5283
|
203
|
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eco:b0002 sfx:S0002 5271
|
204
|
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eco:b0002 sfl:SF0002 5271
|
205
|
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eco:b0002 ecc:c0003 5269
|
206
|
-
|
207
|
-
���ޤ�ư���ʤ����ϡ�
|
208
|
-
|
209
|
-
serv = SOAP::WSDLDriverFactory.new(wsdl).create_rpc_driver
|
210
|
-
serv.wiredump_dev = STDERR # �����ιԤ����
|
211
|
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serv.generate_explicit_type = true
|
212
|
-
|
213
|
-
�Τ褦�� wiredump_dev �� STDERR ����ꤷ���Ԥ��ɲä��Ƽ¹Ԥ��뤳�Ȥǡ�
|
214
|
-
�����ФȤΤ���꤬ɸ�२�顼�˽��Ϥ���ޤ���
|
215
|
-
|
216
|
-
KEGG API v3.0 ���顢�����Ф���ô��ڤ���������ॢ���Ȥ��ɤ���Ū�ǡ�
|
217
|
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���̤η�̤��֤���åɤˤ� offset, limit ������Ƴ�����졢���٤�
|
218
|
-
�������̤ο������¤����褦�ˤʤ�ޤ�����KEGG API v3.0��v5.0 �Ǥ�
|
219
|
-
���줾�� start, max_results �ȸƤФ�Ƥ��ޤ�������KEGG API v6.0 ��
|
220
|
-
offset, limit ��̾���ѹ����ޤ����ˡ����Τ��ᡢ�����Υ�åɤ�
|
221
|
-
���Ƥη�̤����뤿��ˤϥ롼�פ��Ѥ���ɬ�פ�����ޤ���
|
222
|
-
|
223
|
-
#!/usr/bin/env ruby
|
224
|
-
|
225
|
-
require 'soap/wsdlDriver'
|
226
|
-
|
227
|
-
wsdl = "http://soap.genome.jp/KEGG.wsdl"
|
228
|
-
serv = SOAP::WSDLDriverFactory.new(wsdl).create_rpc_driver
|
229
|
-
serv.generate_explicit_type = true
|
230
|
-
|
231
|
-
offset = 1
|
232
|
-
limit = 100
|
233
|
-
|
234
|
-
loop do
|
235
|
-
results = serv.get_best_neighbors_by_gene('eco:b0002', offset, limit)
|
236
|
-
break unless results # ��̤��֤äƤ��ʤ���н�λ
|
237
|
-
results.each do |hit|
|
238
|
-
print hit.genes_id1, "\t", hit.genes_id2, "\t", hit.sw_score, "\n"
|
239
|
-
end
|
240
|
-
offset += limit
|
241
|
-
end
|
242
|
-
|
243
|
-
WSDL ���Ѥ��Ƥ��뤿�ᡢ��������Ǥ� Ruby �ξ��Ͻ�ʬ�˴�ñ�˽�
|
244
|
-
������((<BioRuby|URL:http://bioruby.org/>)) ��Ȥ��Ȥ���˥��å����
|
245
|
-
���Ȥ��Ǥ��ޤ���
|
246
|
-
|
247
|
-
#!/usr/bin/env ruby
|
248
|
-
|
249
|
-
require 'bio'
|
250
|
-
|
251
|
-
serv = Bio::KEGG::API.new
|
252
|
-
|
253
|
-
results = serv.get_all_best_neighbors_by_gene('eco:b0002')
|
254
|
-
results.each do |hit|
|
255
|
-
print hit.genes_id1, "\t", hit.genes_id2, "\t", hit.sw_score, "\n"
|
256
|
-
end
|
257
|
-
|
258
|
-
BioRuby �Ǥ� 'get_all_best_neighbors_by_gene' ��åɤ��������Ƥ��ꡢ
|
259
|
-
��ư�Ǿ嵭����Υ롼�פ�����Ƥη�̤��֤��Ƥ���ޤ����ޤ�������
|
260
|
-
������̾���Υꥹ�Ȥ��Ϥ����б������ͤ�������֤��Ƥ���� filter ���
|
261
|
-
�ɤ�Ȥ����Ȥ�Ǥ��ޤ���
|
262
|
-
|
263
|
-
#!/usr/bin/env ruby
|
264
|
-
|
265
|
-
require 'bio'
|
266
|
-
|
267
|
-
serv = Bio::KEGG::API.new
|
268
|
-
|
269
|
-
results = serv.get_all_best_neighbors_by_gene('eco:b0002')
|
270
|
-
|
271
|
-
# �ߤ����ͤ�������̾�Υڥ��� SW �����������ξ�����
|
272
|
-
fields = [:genes_id1, :genes_id2, :sw_score]
|
273
|
-
results.each do |hit|
|
274
|
-
puts hit.filter(fields).join("\t")
|
275
|
-
end
|
276
|
-
|
277
|
-
# ���줾��ΰ����Ҥǥ��饤���Ȥ��줿�ݥ������ʤɤ�ɽ����������
|
278
|
-
fields1 = [:genes_id1, :start_position1, :end_position1, :best_flag_1to2]
|
279
|
-
fields2 = [:genes_id2, :start_position2, :end_position2, :best_flag_2to1]
|
280
|
-
results.each do |hit|
|
281
|
-
print "> score: ", hit.sw_score, ", identity: ", hit.identity, "\n"
|
282
|
-
print "1:\t", hit.filter(fields1).join("\t"), "\n"
|
283
|
-
print "2:\t", hit.filter(fields2).join("\t"), "\n"
|
284
|
-
end
|
285
|
-
|
286
|
-
���ϡ���IJ�� (eco) ���Ф��� KEGG �ѥ��������ΰ������֤���Ǥ���
|
287
|
-
|
288
|
-
#!/usr/bin/env ruby
|
289
|
-
|
290
|
-
require 'bio'
|
291
|
-
|
292
|
-
serv = Bio::KEGG::API.new
|
293
|
-
|
294
|
-
list = serv.list_pathways("eco")
|
295
|
-
list.each do |path|
|
296
|
-
print path.entry_id, "\t", path.definition, "\n"
|
297
|
-
end
|
298
|
-
|
299
|
-
ArrayOfDefinition �����֤����Τǡ����줾��ˤĤ��� Definition ������
|
300
|
-
�� entry_id (�ѥ���������ID) �� definition (�ѥ��������Υ����ȥ�) ���
|
301
|
-
��Ф��ޤ������ SSDB ����⡢�¤� SSDBRelation �������� genes_id1 ��
|
302
|
-
sw_score �ʤɤ���Ф��Ƥ����ΤǤ����ˡ�
|
303
|
-
|
304
|
-
�Ǹ����ϡ���IJ�ݤΰ����� b1002 �� b2388 ���б�����ܥå����˿����դ�
|
305
|
-
���ѥ������� eco00010 �β������������ơ��ե��������¸������Ǥ���
|
306
|
-
|
307
|
-
#!/usr/bin/env ruby
|
308
|
-
|
309
|
-
require 'bio'
|
310
|
-
|
311
|
-
serv = Bio::KEGG::API.new
|
312
|
-
|
313
|
-
genes = ["eco:b1002", "eco:b2388"]
|
314
|
-
url = serv.mark_pathway_by_objects("path:eco00010", genes)
|
315
|
-
|
316
|
-
puts url
|
317
|
-
|
318
|
-
# BioRuby �ξ�硢���������������¸����Τ� save_image ��åɤ��Ȥ���
|
319
|
-
serv.save_image(url, "filename.gif")
|
320
|
-
|
321
|
-
=== Perl ��
|
322
|
-
|
323
|
-
Perl �Ǥϡ��ʲ��Υ饤�֥����ɲå��ȡ��뤷�Ƥ���ɬ�פ�����ޤ���
|
324
|
-
|
325
|
-
* ((<SOAP::Lite|URL://www.soaplite.com/>)) (Ver. 0.60 ��ư���ǧ)
|
326
|
-
* �������� 0.60 ��꿷�����С������ǤϤ����Ĥ��Υ�åɤ��Ȥ��ʤ��褦�Ǥ�
|
327
|
-
* ((<MIME-Base64|URL:http://search.cpan.org/author/GAAS/MIME-Base64/>))
|
328
|
-
* ((<libwww-perl|URL:http://search.cpan.org/author/GAAS/libwww-perl/>))
|
329
|
-
* ((<URI|URL:http://search.cpan.org/author/GAAS/URI/>))
|
330
|
-
|
331
|
-
�ʲ���Ruby �κǽ�����Ʊ��������¹Ԥ��륵��ץ륳���ɤǤ���
|
332
|
-
|
333
|
-
#!/usr/bin/env perl
|
334
|
-
|
335
|
-
use SOAP::Lite;
|
336
|
-
|
337
|
-
$wsdl = 'http://soap.genome.jp/KEGG.wsdl';
|
338
|
-
|
339
|
-
$serv = SOAP::Lite -> service($wsdl);
|
340
|
-
|
341
|
-
$offset = 1;
|
342
|
-
$limit = 5;
|
343
|
-
|
344
|
-
$top5 = $serv->get_best_neighbors_by_gene('eco:b0002', $offset, $limit);
|
345
|
-
|
346
|
-
foreach $hit (@{$top5}) {
|
347
|
-
print "$hit->{genes_id1}\t$hit->{genes_id2}\t$hit->{sw_score}\n";
|
348
|
-
}
|
349
|
-
|
350
|
-
Ʊ��������IJ�ݤ� KEGG �ѥ��������Υꥹ�Ȥ��֤���Ǥ���
|
351
|
-
|
352
|
-
#!/usr/bin/env perl
|
353
|
-
|
354
|
-
use SOAP::Lite;
|
355
|
-
|
356
|
-
$wsdl = 'http://soap.genome.jp/KEGG.wsdl';
|
357
|
-
|
358
|
-
$results = SOAP::Lite
|
359
|
-
-> service($wsdl)
|
360
|
-
-> list_pathways("eco");
|
361
|
-
|
362
|
-
foreach $path (@{$results}) {
|
363
|
-
print "$path->{entry_id}\t$path->{definition}\n";
|
364
|
-
}
|
365
|
-
|
366
|
-
SOAP::Lite �Ǥϰ�����������Ϥ����ˤϡ�
|
367
|
-
|
368
|
-
SOAP::Data->type(array => [value1, value2, .. ])
|
369
|
-
|
370
|
-
�Τ褦���Ѵ�����ɬ�פ�����Τ����դ�ɬ�פǤ������Ȥ��Хѥ��������ؤο�
|
371
|
-
�Ť��ǰ����ҤΥꥹ�Ȥ��Ϥ����ϡ�
|
372
|
-
|
373
|
-
#!/usr/bin/env perl
|
374
|
-
|
375
|
-
use SOAP::Lite;
|
376
|
-
|
377
|
-
$wsdl = 'http://soap.genome.jp/KEGG.wsdl';
|
378
|
-
|
379
|
-
$serv = SOAP::Lite -> service($wsdl);
|
380
|
-
|
381
|
-
$genes = SOAP::Data->type(array => ["eco:b1002", "eco:b2388"]);
|
382
|
-
|
383
|
-
$result = $serv -> mark_pathway_by_objects("path:eco00010", $genes);
|
384
|
-
|
385
|
-
print $result;
|
386
|
-
|
387
|
-
�Τ褦�ˤʤ�ޤ���
|
388
|
-
|
389
|
-
=== Perl ��������
|
390
|
-
|
391
|
-
KEGG API �ˤ�ʸ�������ͤ����������˼���åɤ������Ĥ�����ޤ�����
|
392
|
-
���Ѥ��� SOAP::Lite �ΥС������˱����ơ�ɬ���ʲ��Τɤ��餫���н褬ɬ�פǤ���
|
393
|
-
|
394
|
-
==== SOAP::Lite v0.60 �ޤ�
|
395
|
-
|
396
|
-
Perl ������ (array) ���֥������Ȥ�����Ȥ��� KEGG API ���Ϥ����ϡ�
|
397
|
-
ɬ���ʲ��Τ褦�� SOAP ���֥������Ȥ�����Ū���Ѵ�����ɬ�פ�����ޤ���
|
398
|
-
|
399
|
-
SOAP::Data->type(array => [value1, value2, ... ])
|
400
|
-
|
401
|
-
==== SOAP::Lite v0.61 �ʹ�
|
402
|
-
|
403
|
-
SOAP::Lite v0.68 �ޤǤϥХ�������ޤ��Τ� v0.69 �ʹߤ����Ѥ��ᤷ�ޤ���
|
404
|
-
|
405
|
-
Perl ��ʸ���� (string) ����� (int) ������ (array) ���֥������Ȥ�
|
406
|
-
ArrayOfstring �� ArrayOfint ���� SOAP ���֥������Ȥ��Ѵ�����
|
407
|
-
���֥롼����������ɲä���ɬ�פ�����ޤ���
|
408
|
-
|
409
|
-
sub SOAP::Serializer::as_ArrayOfstring{
|
410
|
-
my ($self, $value, $name, $type, $attr) = @_;
|
411
|
-
|
412
|
-
return [$name, {'xsi:type' => 'array', %$attr}, $value];
|
413
|
-
}
|
414
|
-
|
415
|
-
sub SOAP::Serializer::as_ArrayOfint{
|
416
|
-
my ($self, $value, $name, $type, $attr) = @_;
|
417
|
-
return [$name, {'xsi:type' => 'array', %$attr}, $value];
|
418
|
-
}
|
419
|
-
|
420
|
-
�ޤ���������ץ���ˤ��������Ƥ������Ȥǡ�
|
421
|
-
|
422
|
-
$genes = SOAP::Data->type(array => ["eco:b1002", "eco:b2388"]);
|
423
|
-
|
424
|
-
�ǤϤʤ�
|
425
|
-
|
426
|
-
$genes = ["eco:b1002", "eco:b2388"];
|
427
|
-
|
428
|
-
�Τ褦�˾�ά���ƽ��Ȥ��Ǥ���褦�ˤʤ�ޤ��ʾ�ά���ʤ��Ƥ���ޤ���ˡ�
|
429
|
-
|
430
|
-
==== �ƥ��ȥץ������
|
431
|
-
|
432
|
-
SOAP::Lite v0.69 �� ArrayOfstring ���Ѵ������ޤ�Ư���Ƥ��뤫�ɤ�����
|
433
|
-
�ʲ��Υץ������ǥƥ��ȤǤ��ޤ��������� URL ��ɽ�������� OK �Ǥ���
|
434
|
-
|
435
|
-
#!/usr/bin/env perl
|
436
|
-
|
437
|
-
use SOAP::Lite +trace => [qw(debug)];
|
438
|
-
|
439
|
-
print "SOAP::Lite = ", $SOAP::Lite::VERSION, "\n";
|
440
|
-
|
441
|
-
my $serv = SOAP::Lite -> service("http://soap.genome.jp/KEGG.wsdl");
|
442
|
-
|
443
|
-
my $result = $serv->mark_pathway_by_objects("map:eco00010", $genes);
|
444
|
-
print $result, "\n";
|
445
|
-
|
446
|
-
# sub routines implicitly used in the above code
|
447
|
-
|
448
|
-
sub SOAP::Serializer::as_ArrayOfstring{
|
449
|
-
my ($self, $value, $name, $type, $attr) = @_;
|
450
|
-
return [$name, {'xsi:type' => 'array', %$attr}, $value];
|
451
|
-
}
|
452
|
-
|
453
|
-
sub SOAP::Serializer::as_ArrayOfint{
|
454
|
-
my ($self, $value, $name, $type, $attr) = @_;
|
455
|
-
return [$name, {'xsi:type' => 'array', %$attr}, $value];
|
456
|
-
}
|
457
|
-
|
458
|
-
=== Python ��
|
459
|
-
|
460
|
-
Python �Ǥϰʲ��Υ饤�֥����ɲå��ȡ��뤷�Ƥ���ɬ�פ�����ޤ���
|
461
|
-
|
462
|
-
* ((<SOAPpy|URL:http://pywebsvcs.sourceforge.net/>))
|
463
|
-
|
464
|
-
�ޤ���SOAPpy ����¸���Ƥ��뤤���Ĥ��Υѥå����� (fpconst, PyXML �ʤ�) ��
|
465
|
-
ɬ�פˤʤ�ޤ���
|
466
|
-
|
467
|
-
�ʲ���KEGG/PATHWAY �� 00020 �֤Υѥ��������˺ܤäƤ�����IJ�ݤΰ����Ҥ�
|
468
|
-
�ꥹ�Ȥ��֤�����ץ륳���ɤǤ���
|
469
|
-
|
470
|
-
#!/usr/bin/env python
|
471
|
-
|
472
|
-
from SOAPpy import WSDL
|
473
|
-
|
474
|
-
wsdl = 'http://soap.genome.jp/KEGG.wsdl'
|
475
|
-
serv = WSDL.Proxy(wsdl)
|
476
|
-
|
477
|
-
results = serv.get_genes_by_pathway('path:eco00020')
|
478
|
-
print results
|
479
|
-
|
480
|
-
=== Java ��
|
481
|
-
|
482
|
-
Java �Ǥ� Apache Axis �饤�֥��� axis-1.2alpha ��꿷�����С������
|
483
|
-
(axis-1_1 �ǤϤ��ޤ�ư���ޤ���ˤ����ꤷ�ơ�ɬ�פ� jar �ե������Ŭ��
|
484
|
-
�ʥǥ��쥯�ȥ���֤��Ƥ���ɬ�פ�����ޤ���
|
485
|
-
|
486
|
-
* ((<Apache Axis|URL:http://ws.apache.org/axis/>))
|
487
|
-
|
488
|
-
���Ȥ��� Apache Axis �С������ axis-1_2beta �ΥХ��ʥ����ۤξ�硢
|
489
|
-
axis-1_2beta/lib �ʲ��ˤ��� jar �ե�����ȡ�����Υǥ��쥯��
|
490
|
-
��˥��ԡ����ޤ���
|
491
|
-
|
492
|
-
% cp axis-1_2beta/lib/* /path/to/lib/
|
493
|
-
|
494
|
-
�ʲ��Τ褦�˼¹Ԥ��� WSDL ���� KEGG API �ѤΥ��饹��ư�������ޤ���
|
495
|
-
�ޤ����������줿�ե�������Զ���ľ������ˡ�
|
496
|
-
((<axisfix.pl|URL:http://www.genome.jp/kegg/soap/support/axisfix.pl>))
|
497
|
-
������ץȤ����ꤷ�Ƥ����ޤ���
|
498
|
-
|
499
|
-
% 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
|
500
|
-
% perl -i axisfix.pl keggapi/KEGGBindingStub.java
|
501
|
-
% javac -classpath /path/to/lib/axis.jar:/path/to/lib/jaxrpc.jar:/path/to/lib/wsdl4j.jar:. keggapi/KEGGLocator.java
|
502
|
-
% jar cvf keggapi.jar keggapi/*
|
503
|
-
% javadoc -classpath /path/to/lib/axis.jar:/path/to/lib/jaxrpc.jar -d keggapi_javadoc keggapi/*.java
|
504
|
-
|
505
|
-
javadoc �αѸ��Ǥ�ɬ�פʾ��� javadoc �� -locale en_US ���ץ�����
|
506
|
-
�Ĥ��Ƽ¹Ԥ��ޤ���
|
507
|
-
|
508
|
-
�ʲ��ϡ�Python �����Ʊ�ͤˡ����ꤷ�� KEGG/PATHWAY �˺ܤäƤ�������Ҥ�
|
509
|
-
�ꥹ�Ȥ�ɽ�����륵��ץ륳���ɤǤ���
|
510
|
-
|
511
|
-
import keggapi.*;
|
512
|
-
|
513
|
-
class GetGenesByPathway {
|
514
|
-
public static void main(String[] args) throws Exception {
|
515
|
-
KEGGLocator locator = new KEGGLocator();
|
516
|
-
KEGGPortType serv = locator.getKEGGPort();
|
517
|
-
|
518
|
-
String query = args[0];
|
519
|
-
String[] results = serv.get_genes_by_pathway(query);
|
520
|
-
|
521
|
-
for (int i = 0; i < results.length; i++) {
|
522
|
-
System.out.println(results[i]);
|
523
|
-
}
|
524
|
-
}
|
525
|
-
}
|
526
|
-
|
527
|
-
���ϡ�SSDBRelation ����������äƤ�����Ǥ���
|
528
|
-
|
529
|
-
import keggapi.*;
|
530
|
-
|
531
|
-
class GetBestNeighborsByGene {
|
532
|
-
public static void main(String[] args) throws Exception {
|
533
|
-
KEGGLocator locator = new KEGGLocator();
|
534
|
-
KEGGPortType serv = locator.getKEGGPort();
|
535
|
-
|
536
|
-
String query = args[0];
|
537
|
-
SSDBRelation[] results = null;
|
538
|
-
|
539
|
-
results = serv.get_best_neighbors_by_gene(query, 1, 50);
|
540
|
-
|
541
|
-
for (int i = 0; i < results.length; i++) {
|
542
|
-
String gene1 = results[i].getGenes_id1();
|
543
|
-
String gene2 = results[i].getGenes_id2();
|
544
|
-
int score = results[i].getSw_score();
|
545
|
-
System.out.println(gene1 + "\t" + gene2 + "\t" + score);
|
546
|
-
}
|
547
|
-
}
|
548
|
-
}
|
549
|
-
|
550
|
-
���Υץ������ϰʲ��Τ褦�� -classpath ���ץ����� keggapi.jar �ե�
|
551
|
-
�����ä��ƥ���ѥ��롢�¹Ԥ��ޤ���
|
552
|
-
|
553
|
-
% javac -classpath /path/to/lib/axis.jar:/path/to/lib/jaxrpc.jar:/path/to/lib/wsdl4j.jar:/path/to/keggapi.jar GetBestNeighborsByGene.java
|
554
|
-
|
555
|
-
% 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
|
556
|
-
|
557
|
-
�Ķ��ѿ� CLASSPATH ����ꤷ�Ƥ����ȡ�Ĺ�����ץ���������ɬ�פ���
|
558
|
-
���ʤ�ޤ���
|
559
|
-
|
560
|
-
bash �ޤ��� zsh �ξ�硧
|
561
|
-
|
562
|
-
% for i in /path/to/lib/*.jar
|
563
|
-
do
|
564
|
-
CLASSPATH="${CLASSPATH}:${i}"
|
565
|
-
done
|
566
|
-
% export CLASSPATH
|
567
|
-
|
568
|
-
tcsh �ξ�硧
|
569
|
-
|
570
|
-
% foreach i ( /path/to/lib/*.jar )
|
571
|
-
setenv CLASSPATH ${CLASSPATH}:${i}
|
572
|
-
end
|
573
|
-
|
574
|
-
¾������ͤȷ����Ȥ��ͤμ��Ф����ʤɤˤĤ��Ƥϡ�WSDL2Java �ˤ������
|
575
|
-
���줿�ʲ��Υɥ�����ȤȤ��Ƥ���������
|
576
|
-
|
577
|
-
* ((<URL:http://www.genome.jp/kegg/soap/doc/keggapi_javadoc_ja/>))
|
578
|
-
|
579
|
-
== KEGG API ��ե����
|
580
|
-
|
581
|
-
�ʲ��Ǥϡ�KEGG API ��Ȥ��Τ�ɬ�פʾ�������ƤΥ�åɤ���⤷�ޤ���
|
582
|
-
|
583
|
-
=== WSDL �ե�����
|
584
|
-
|
585
|
-
SOAP �Ǥϡ������Ф��ɤΤ褦�ʥ�åɤ���äƤ��뤫�ΤäƤ���ɬ�פ�
|
586
|
-
����ޤ�����WSDL ��Ȥ��Ȥ��μ���ư���Ǥ��ޤ���WSDL �ե������
|
587
|
-
�������ƥ��饤����ȥɥ饤�Ф���������Ȥ����ޤǡ��̾�� SOAP/WSDL ��
|
588
|
-
�饤�֥�꤬�������Ƥ����Ϥ��Ǥ���KEGG API �� WSDL �ե�����ϰʲ���
|
589
|
-
URL �ˤ���ޤ���
|
590
|
-
|
591
|
-
* ((<URL:http://soap.genome.jp/KEGG.wsdl>))
|
592
|
-
|
593
|
-
=== �Ѹ������
|
594
|
-
|
595
|
-
�ʲ��β���ǽФƤ��� KEGG ��Ϣ�Ѹ�������Ƥ����ޤ���
|
596
|
-
|
597
|
-
* org �� KEGG �˴ޤޤ�Ƥ�����ʪ��줾�죳ʸ�������ɤ�
|
598
|
-
ɽ��������Τǡ�eco ����IJ�ݡ�sce ���в����ʤɤȤʤäƤ��ޤ���
|
599
|
-
��ʸ�������ɤΥꥹ�Ȥ� list_organisms ��åɤ�ʲ��Υڡ�����
|
600
|
-
���Ȥ��Ƥ���������
|
601
|
-
|
602
|
-
* ((<URL:http://www.genome.jp/kegg/catalog/org_list.html>))
|
603
|
-
|
604
|
-
* db �� GenomeNet ������Ƥ���ǡ����١���̾�Ǥ����ǡ����١���̾��
|
605
|
-
�ꥹ�ȤˤĤ��Ƥ� list_databases ��åɤȤ��Ƥ���������
|
606
|
-
|
607
|
-
* entry_id �� db_name �ȥ���ȥ�̾�� ':' �Ƿ�礷�����ƤΥǡ����١����֤�
|
608
|
-
��ˡ����� ID �Ǥ������Ȥ��� embl:J00231 �� EMBL �Υ���ȥ� J00231 ��
|
609
|
-
�ؤ��ޤ���entry_id �ϡ��ʲ��� genes_id, enzyme_id, compound_id,
|
610
|
-
drug_id, glycan_id, reaction_id, pathway_id, motif_id �ʤɤ�ޤߤޤ���
|
611
|
-
|
612
|
-
* genes_id �� keggorg �Ȱ�����̾�� ':' �Ƿ�礷�� KEGG �ΰ����� ID �Ǥ���
|
613
|
-
eco:b0001 ����IJ�ݤΰ����� b0001 ��ؤ��ޤ���
|
614
|
-
|
615
|
-
* enzyme_id �� ec: ��Ĥ��������ֹ�� ID �Ǥ���ec:1.1.1.1 �Ϲ����ֹ�
|
616
|
-
1.1.1.1 �ι��ǤǤ��륢�륳���롦�ǥҥɥ����ʡ�����ؤ��ޤ���
|
617
|
-
|
618
|
-
* compound_id �� cpd: ��Ĥ�������ʪ�� ID �Ǥ���cpd:C00158 �ϲ���ʪ�ֹ�
|
619
|
-
C00158 �β���ʪ�Ǥ��륯�������ؤ��ޤ���
|
620
|
-
|
621
|
-
* drug_id �� dr: ��Ĥ�������ʪ�� ID �Ǥ���dr:D00201 �ϥɥ�å��ֹ�
|
622
|
-
D00201 �Υɥ�å��Ǥ���ƥȥ饵��������ؤ��ޤ���
|
623
|
-
|
624
|
-
* glycan_id �� gl: ��Ĥ�������ʪ�� ID �Ǥ���gl:G00050 �������ֹ�
|
625
|
-
G00050 �������Ǥ��� Paragloboside ��ؤ��ޤ���
|
626
|
-
|
627
|
-
* reaction_id �� REACTION �ǡ����١����Υ���ȥ��ֹ�ǡ�rn:R00959 ��
|
628
|
-
�ꥢ��������ֹ� R00959 ��ȿ�� (cpd:C00103 �� cpd:00668 �֤��Ѵ�) ��
|
629
|
-
�ؤ��ޤ���
|
630
|
-
|
631
|
-
* pathway_id �� KEGG/PATHWAY �ǡ����١����Υѥ��������ֹ�ǡ��ѥ�������
|
632
|
-
�ֹ�Υץ�ե��å����� map �ξ��ϥ�ե���ѥ���������keggorg ��
|
633
|
-
���Ϥ�����ʪ��λ��İ����Ҥκܤä��ѥ���������ɽ���ޤ����㤨��
|
634
|
-
path:map00020 �ϥ�ե���ѥ��������� 00020 �֤�path:eco00020 ��
|
635
|
-
��IJ�ݤΥѥ������� 00020 �֤�ؤ��ޤ���
|
636
|
-
|
637
|
-
* motif_id �ϥ�����եǡ����١����Υ���ȥ�̾�ǡ�pf:DnaJ �� Pfam �Υ���ȥ�
|
638
|
-
DnaJ ��ؤ��ޤ���'pf' ��¾��'ps' �� PROSITE, 'bl' �� BLOCS, 'pr' ��
|
639
|
-
PRINTS, 'pd' �� PRODOM ��ؤ��ޤ���
|
640
|
-
|
641
|
-
* ko_id �� KO (KEGG Orthology) �ǡ����١����Υ���ȥ��ֹ�ǡ�ko:K02598
|
642
|
-
�� KO �ֹ� K02598 �� nitrite transporter NirC �Υ������������ʰ�����
|
643
|
-
���롼�פ�ؤ��ޤ���
|
644
|
-
|
645
|
-
* ko_class_id �� KO ����Ū��ʬ�ष���Ƴ��ءʥ��饹�ˤ� ID �ǡ�
|
646
|
-
'01110' �� Carbohydrate Metabolism ���饹�ˤʤ�ޤ���
|
647
|
-
KO ���饹�� KO �ֹ�Υꥹ�Ȥϰʲ��Υڡ����Ȥ��Ƥ���������
|
648
|
-
|
649
|
-
* ((<URL:http://www.genome.jp/dbget-bin/get_htext?KO>))
|
650
|
-
|
651
|
-
* offset, limit �ϰ��٤��֤äƤ����̤ο�����ꤹ�륪�ץ����ǡ�
|
652
|
-
offset ���ܤ��� limit �Ĥη�̤�������ޤ������Ƥη�̤�����ˤ�
|
653
|
-
offset = offset + limit �Ȥ��ƶ��������֤äƤ���ޤǷ����֤�
|
654
|
-
��åɤ�ƤӤޤ���
|
655
|
-
|
656
|
-
* fg_color_list �ϥѥ��������ؤο��Ť��ǥ��֥������Ȥ��Ȥ�ʸ����������
|
657
|
-
������ꤹ������Ǥ���
|
658
|
-
|
659
|
-
* fg_color_list �ϥѥ��������ؤο��Ť��ǥ��֥������Ȥ��Ȥ��طʤ�
|
660
|
-
������ꤹ������Ǥ���
|
661
|
-
|
662
|
-
��Ϣ URL��
|
663
|
-
* ((<URL:http://www.genome.jp/kegg/kegg3.html>))
|
664
|
-
|
665
|
-
=== ����ͤΥǡ�����
|
666
|
-
|
667
|
-
KEGG API �Υ�åɤ�ʸ����ʤ�ñ����ͤ��֤���Τ����Ǥʤ���ʣ���ʥǡ���
|
668
|
-
��¤����ä��ͤ��֤����⤢�ꡢ���Τ���Υǡ��������������Ƥ��ޤ���
|
669
|
-
API �Υ�åɤˤ��ʸ����ʤɤΡ˷�̤��ʤ��ä���硢���ˤ�äưʲ���
|
670
|
-
����ͤ��֤���ޤ���
|
671
|
-
* �������� -- ��Ȥ�� ArrayOfOBJ �ʥ��֥������Ȥ�����ˤ��֤���åɤξ��
|
672
|
-
* ����ʸ���� -- ��Ȥ�� String ��ʸ����ˤ��֤���åɤξ��
|
673
|
-
* -1 -- ��Ȥ�� int �ʿ��͡ˤ��֤���åɤξ��
|
674
|
-
* NULL -- ��Ȥ�Ȱʲ���������줿���֥������ȤΤɤ줫���֤���åɤξ��
|
675
|
-
|
676
|
-
+ SSDBRelation ��
|
677
|
-
|
678
|
-
SSDB �ǡ����١����γƥե�����ɤ��б������ͤ����ä��ǡ������Ǥ���
|
679
|
-
|
680
|
-
genes_id1 ������� genes_id (string)
|
681
|
-
genes_id2 �������åȤ� genes_id (string)
|
682
|
-
sw_score genes_id1 �� genes_id2 �֤� Smith-Waterman ������ (int)
|
683
|
-
bit_score genes_id1 �� genes_id2 �֤� bit ������ (float)
|
684
|
-
identity genes_id1 �� genes_id2 �֤� �����ǥ�ƥ��ƥ� (float)
|
685
|
-
overlap genes_id1 �� genes_id2 �Υ����С���å��ΰ��Ĺ�� (int)
|
686
|
-
start_position1 genes_id1 �Υ��饤���Ȥγ��ϻĴ���� (int)
|
687
|
-
end_position1 genes_id1 �Υ��饤���Ȥν�ü�Ĵ���� (int)
|
688
|
-
start_position2 genes_id2 �Υ��饤���Ȥγ��ϻĴ���� (int)
|
689
|
-
end_position2 genes_id2 �Υ��饤���Ȥν�ü�Ĵ���� (int)
|
690
|
-
best_flag_1to2 genes_id1 ���鸫�� genes_id2 ���٥��ȥҥåȤ� (boolean)
|
691
|
-
best_flag_2to1 genes_id2 ���鸫�� genes_id1 ���٥��ȥҥåȤ� (boolean)
|
692
|
-
definition1 genes_id1 �Υǥե��˥����ʸ���� (string)
|
693
|
-
definition2 genes_id2 �Υǥե��˥����ʸ���� (string)
|
694
|
-
length1 genes_id1 �Υ��ߥλ������Ĺ�� (int)
|
695
|
-
length2 genes_id2 �Υ��ߥλ������Ĺ�� (int)
|
696
|
-
|
697
|
-
+ ArrayOfSSDBRelation ��
|
698
|
-
|
699
|
-
ʣ���� SSDBRelation ���ǡ�����ޤ�����Ǥ���
|
700
|
-
|
701
|
-
+ MotifResult ��
|
702
|
-
|
703
|
-
motif_id ������եǡ����١����Υ���ȥ� ID (string)
|
704
|
-
definition ������դΥǥե��˥���� (string)
|
705
|
-
genes_id ������դ���äƤ�������Ҥ� genes_id (string)
|
706
|
-
start_position ������դγ��ϻĴ���� (int)
|
707
|
-
end_position ������դν�λ�Ĵ���� (int)
|
708
|
-
score ������� (PROSITE Profile, TIGRFAM) ������ (float)
|
709
|
-
evalue ������� (Pfam) �� E-value (double)
|
710
|
-
|
711
|
-
����score �� evalue �Τ������б������ͤ�̵����ΤˤĤ��Ƥ� -1 ���֤��ޤ���
|
712
|
-
|
713
|
-
+ ArrayOfMotifResult ��
|
714
|
-
|
715
|
-
ʣ���� MotifResult ���ǡ�����ޤ�����Ǥ���
|
716
|
-
|
717
|
-
+ Definition ��
|
718
|
-
|
719
|
-
entry_id �ǡ����١�������ȥ��ID (string)
|
720
|
-
definition ����ȥ�Υǥե��˥������� (string)
|
721
|
-
|
722
|
-
+ ArrayOfDefinition ��
|
723
|
-
|
724
|
-
ʣ���� Definitioin ���ǡ�����ޤ�����Ǥ���
|
725
|
-
|
726
|
-
+ LinkDBRelation ��
|
727
|
-
|
728
|
-
entry_id1 �ǡ����١����Υ���ȥ� ID (string)
|
729
|
-
entry_id2 �ǡ����١����Υ���ȥ� ID (string)
|
730
|
-
type "direct" �ޤ��� "indirect" �Υ�μ��� (string)
|
731
|
-
path ��η�ϩ (string)
|
732
|
-
|
733
|
-
+ ArrayOfLinkDBRelation ��
|
734
|
-
|
735
|
-
ʣ���� LinkDBRelation ���ǡ�����ޤ�����Ǥ���
|
736
|
-
|
737
|
-
+ PathwayElement ��
|
738
|
-
|
739
|
-
�ѥ����������������Ƥ���ġ���Ȣ��ݤʤɤΥ��֥������Ȥ�ɽ���ǡ������Ǥ���
|
740
|
-
|
741
|
-
element_id �ѥ���������Υ��֥������Ȥ�ؤ���ˡ����� ID (int)
|
742
|
-
type ���֥������Ȥμ��� ("gene", "enzyme" �ʤ�) (string)
|
743
|
-
names ���֥������ȤˤĤ���줿̾���Υꥹ�� (ArrayOfstring)
|
744
|
-
components ���롼�פξ��ʤɴޤޤ�륪�֥������ȤΥꥹ�� (ArrayOfint)
|
745
|
-
|
746
|
-
+ ArrayOfPathwayElement ��
|
747
|
-
|
748
|
-
ʣ���� PathwayElement ���ǡ�����ޤ�����Ǥ���
|
749
|
-
|
750
|
-
+ PathwayElementRelation ��
|
751
|
-
|
752
|
-
PathwayElement �֤δط���ɽ���ǡ������Ǥ���
|
753
|
-
|
754
|
-
element_id1 �ѥ���������Υ��֥������Ȥ�ؤ���ˡ����� ID (int)
|
755
|
-
element_id2 �ѥ���������Υ��֥������Ȥ�ؤ���ˡ����� ID (int)
|
756
|
-
type �ط��μ��� ("ECrel", "maplink" �ʤ�) (string)
|
757
|
-
subtypes �ط��˴ؤ�륪�֥������Ȥ����� (ArrayOfSubtype)
|
758
|
-
|
759
|
-
+ ArrayOfPathwayElementRelation ��
|
760
|
-
|
761
|
-
ʣ���� PathwayElementRelation ���ǡ�����ޤ�����Ǥ���
|
762
|
-
|
763
|
-
++ Subtype ��
|
764
|
-
|
765
|
-
PathwayElementRelation ������ǻȤ�������Ǥǡ�PathwayElement �֤�
|
766
|
-
�ط��Ť��륪�֥������ȡʲ���ʪ�ʤɡˤ�ɽ���ǡ������Ǥ���
|
767
|
-
|
768
|
-
element_id �ѥ���������Υ��֥������Ȥ�ؤ���ˡ����� ID (int)
|
769
|
-
relation �ط��μ��� ("compound", "inhibition" �ʤ�) (string)
|
770
|
-
type �ط��ε��� ("+p", "--|" �ʤ�) (string)
|
771
|
-
|
772
|
-
++ ArrayOfSubtype ��
|
773
|
-
|
774
|
-
ʣ���� PathwayElementRelation ���ǡ�����ޤ�����Ǥ���
|
775
|
-
|
776
|
-
+ StructureAlignment ��
|
777
|
-
|
778
|
-
�桼���λ��ꤷ�����ع�¤�ȥǡ����١�����ι�¤����Ӥ�������
|
779
|
-
���饤����ȤΥ��������б�����Ρ��ɡʸ��ǡˤΥꥹ�Ȥ�ɽ��
|
780
|
-
�ǡ������Ǥ���
|
781
|
-
|
782
|
-
target_id ��¤����оݤΥ���ȥ� ID (string)
|
783
|
-
score ��¤��ӤΥ����� (float)
|
784
|
-
query_nodes ���Ϲ�¤��ǥ��饤����Ȥ��줿�Ρ����ֹ� (ArrayOfint)
|
785
|
-
target_nodes �оݹ�¤����б�����Ρ����ֹ� (ArrayOfint)
|
786
|
-
|
787
|
-
+ ArrayOfStructureAlignment ��
|
788
|
-
|
789
|
-
ʣ���� StructureAlignment ���ǡ�����ޤ�����Ǥ���
|
790
|
-
|
791
|
-
=== ��åɰ���
|
792
|
-
|
793
|
-
�ʲ���KEGG API ������åɤΥꥹ�ȤǤ�����åɤˤϥ������֤���Τ�
|
794
|
-
�ƥǡ����١������Ф����Τ�����ޤ������ߡ�KEGG �ˤ���ǡ����١����Τ���
|
795
|
-
KEGG API ���оݤȤʤäƤ����Τ� SSDB, PATHWAY, GENES, LIGAND �Ǥ�������
|
796
|
-
�ʳ��Υǡ����١����ؤ��б����åɤ��ɲä�缡�����ʤ�ͽ��Ǥ���
|
797
|
-
|
798
|
-
�ʲ�����Ǥϡ������ʤɤ� Ruby �����ɽ������äƽ�Ƥ��ޤ������ºݤ�
|
799
|
-
�������ä˥ꥹ�Ȥ��Ϥ����ʤɡˤϻ��Ѥ������ˤ�äưۤʤ��ǽ��������ޤ���
|
800
|
-
|
801
|
-
==== �����
|
802
|
-
|
803
|
-
�ǿ��Υǡ����١�������ʤɤ��֤�����Υ�åɤǤ���
|
804
|
-
|
805
|
-
--- list_databases
|
806
|
-
|
807
|
-
KEGG �����Ƥ��륲�Υ�ͥåȤǸ������ѤǤ���ǡ����١����ΰ������֤��ޤ���
|
808
|
-
|
809
|
-
���͡�
|
810
|
-
ArrayOfDefinition (db, definition)
|
811
|
-
|
812
|
-
��Ϣ URL��
|
813
|
-
* ((<URL:http://www.genome.jp/dbget/>))
|
814
|
-
* ((<URL:http://www.genome.jp/about_genomenet/service.html>)) (section 2.2)
|
815
|
-
|
816
|
-
--- list_organisms
|
817
|
-
|
818
|
-
���� KEGG �˴ޤޤ�Ƥ�����ʪ�� (org) �Υꥹ�Ȥ��֤��ޤ���
|
819
|
-
|
820
|
-
���͡�
|
821
|
-
ArrayOfDefinition (org, definition)
|
822
|
-
|
823
|
-
��Ϣ URL��
|
824
|
-
* ((<URL:http://www.genome.jp/kegg/catalog/org_list.html>))
|
825
|
-
* ((<URL:http://www.genome.jp/dbget-bin/get_htext?Organisms+-n>))
|
826
|
-
|
827
|
-
--- list_pathways(string:org)
|
828
|
-
|
829
|
-
���� KEGG �˴ޤޤ�Ƥ�����ꤷ����ʪ�Υѥ��������Υꥹ�Ȥ��֤��ޤ���������
|
830
|
-
'map' �Ȥ���ʸ�����Ϳ����ȥ�ե���ѥ��������Υꥹ�Ȥ��֤��ޤ���
|
831
|
-
|
832
|
-
���͡�
|
833
|
-
ArrayOfDefinition (pathway_id, definition)
|
834
|
-
|
835
|
-
��Ϣ URL��
|
836
|
-
* ((<URL:http://www.genome.jp/kegg/pathway.html>))
|
837
|
-
|
838
|
-
==== DBGET
|
839
|
-
|
840
|
-
DBGET �����ƥ���Ф����åɤΰ����Ǥ���DBGET �ˤĤ��ƾܤ����ϰʲ���
|
841
|
-
�ڡ����Ȥ��Ƥ���������
|
842
|
-
|
843
|
-
��Ϣ URL��
|
844
|
-
* ((<URL:http://www.genome.jp/dbget/dbget_manual.html>))
|
845
|
-
* ((<URL:http://www.genome.jp/dbget-bin/binfo>))
|
846
|
-
|
847
|
-
--- binfo(string:db)
|
848
|
-
|
849
|
-
���ꤷ���ǡ����١����Υ���ȥ���乹�����ʤɾܤ����ǿ�������֤��ޤ���
|
850
|
-
'all' ���Ϥ������Ѳ�ǽ�����ƤΥǡ����١����ξ�����֤��ޤ���
|
851
|
-
binfo ���ޥ�ɤؤΰ�����ʸ������Ϥ��ޤ���
|
852
|
-
|
853
|
-
���͡�
|
854
|
-
string
|
855
|
-
|
856
|
-
�㡧
|
857
|
-
# GenBank �ǡ����١����κǿ�����
|
858
|
-
binfo('gb')
|
859
|
-
# ���ƤΥǡ����١����κǿ�����
|
860
|
-
binfo('all')
|
861
|
-
|
862
|
-
--- bfind(string:str)
|
863
|
-
|
864
|
-
DBGET �� bfind ���ޥ�ɤؤΥ�åѡ��Ǥ���������ɤˤ�ꥨ��ȥ��
|
865
|
-
�������뤳�Ȥ��Ǥ��ޤ������٤�Ϳ�����륭����ɤο��� 100 �İʲ���
|
866
|
-
���¤���Ƥ��ޤ���
|
867
|
-
|
868
|
-
���͡�
|
869
|
-
string
|
870
|
-
|
871
|
-
�㡧
|
872
|
-
# �ǥե��˥����� E-cadherin �� human ����� GenBank �Υ���ȥ��
|
873
|
-
bfind("gb E-cadherin human")
|
874
|
-
|
875
|
-
|
876
|
-
--- bget(string:str)
|
877
|
-
|
878
|
-
���ꤷ�� entry_id �Υ���ȥ���֤��ޤ���GENES �ΰ����ҥ���ȥ��Ϥ��ᡢ
|
879
|
-
���Υ�ͥåȤ� DBGET �����ƥ������Ƥ����͡��ʥǡ����١���
|
880
|
-
(list_databases ��) �Υ���ȥ�����Ƽ����Ǥ��ޤ���bget ���ޥ�ɤؤ�
|
881
|
-
���ޥ�ɥ饤�ץ�����ʸ������Ϥ��ޤ������٤˼����Ǥ��륨��ȥ��
|
882
|
-
���� 100 �İʲ������¤���Ƥ��ޤ���
|
883
|
-
|
884
|
-
���͡�
|
885
|
-
string
|
886
|
-
|
887
|
-
�㡧
|
888
|
-
# ʣ���Υ���ȥ�����
|
889
|
-
bget("eco:b0002 bsu:BG10065 cpd:C00209")
|
890
|
-
# FASTA �ե����ޥåȤΥ��ߥλ���������
|
891
|
-
bget("-f -n a eco:b0002 bsu:BG10065")
|
892
|
-
# FASTA �ե����ޥåȤα�����������
|
893
|
-
bget("-f -n n eco:b0002 hin:tRNA-Cys-1")
|
894
|
-
|
895
|
-
--- btit(string:str)
|
896
|
-
|
897
|
-
DBGET �� btit ���ޥ�ɤؤΥ�åѡ��Ǥ������ꤷ������ȥ�� ID ���б���
|
898
|
-
��ǥե��˥������֤��ޤ������٤�Ϳ�����륨��ȥ�ο��� 100 �İʲ���
|
899
|
-
���¤���Ƥ��ޤ���
|
900
|
-
|
901
|
-
���͡�
|
902
|
-
string
|
903
|
-
|
904
|
-
�㡧
|
905
|
-
# ����飴�Ĥΰ����ҤΥǥե��˥�����
|
906
|
-
btit("hsa:1798 mmu:13478 dme:CG5287-PA cel:Y60A3A.14")
|
907
|
-
|
908
|
-
--- bconv(string:str)
|
909
|
-
|
910
|
-
�����ǡ����١����� ID �� KEGG �� ID ���Ѵ����ޤ���
|
911
|
-
��̤ϡ���������䤤��碌 ID ���Ѵ� ID �Υ����ڤ�ʸ����Ȥ����֤���ޤ���
|
912
|
-
���ߡ��ʲ��γ����ǡ����١������б����Ƥ��ޤ���
|
913
|
-
|
914
|
-
�����ǡ����١��� �ǡ����١���̾�� prefix
|
915
|
-
---------------- -----------------------
|
916
|
-
NCBI GI ncbi-gi:
|
917
|
-
NCBI GeneID ncbi-geneid:
|
918
|
-
GenBank genbank:
|
919
|
-
UniGene unigene:
|
920
|
-
UniProt uniprot:
|
921
|
-
OMIM omim:
|
922
|
-
|
923
|
-
���Ȥ��� UniProt ID �ϡ����Ǥ� KEGG GENES �˵��ܤ���Ƥ��� UniProt
|
924
|
-
�ؤΥ��¾��EBI �� Genome Reviews �˵��ܤ���Ƥ��� UniProt ID
|
925
|
-
�ȥ����������� ID ���б����Ѥ��ơ�NCBI �ȶ��̤Υ����������� ID ��
|
926
|
-
KEGG GENES ���б�ɽ���Ȥ��Ѵ�����Ƥ��ޤ���
|
927
|
-
|
928
|
-
���͡�
|
929
|
-
string
|
930
|
-
|
931
|
-
�㡧
|
932
|
-
# NCBI GI �� Gene ID �� KEGG genes_id ���Ѵ�
|
933
|
-
serv.bconv("ncbi-gi:10047086 ncbi-gi:10047090 ncbi-geneid:14751")
|
934
|
-
|
935
|
-
��Ϣ URL��
|
936
|
-
* ((<URL:http://www.genome.jp/kegg/genes.html>)) (Gene name conversion)
|
937
|
-
|
938
|
-
==== LinkDB
|
939
|
-
|
940
|
-
+ �ǡ����١����֤Υ��
|
941
|
-
|
942
|
-
--- get_linkdb_by_entry(string:entry_id, string:db, int:offset, int:limit)
|
943
|
-
|
944
|
-
���ꤷ�� entry_id ����ľ�ܤޤ��ϴ���Ū�˥����Ƥ��륨��ȥ�η�ϩ��
|
945
|
-
db �ǻ��ꤷ���ǡ����١����ˤ��ɤ��ޤǸ������ޤ���
|
946
|
-
|
947
|
-
���͡�
|
948
|
-
ArrayOfLinkDBRelation
|
949
|
-
|
950
|
-
�㡧
|
951
|
-
# E. coli �ΰ����� b0002 �����Τ��ɤ�� KEGG/PATHWAY �Υ���ȥ��
|
952
|
-
get_linkdb_by_entry('eco:b0002', 'pathway', 1, 10)
|
953
|
-
get_linkdb_by_entry('eco:b0002', 'pathway', 11, 10)
|
954
|
-
|
955
|
-
��Ϣ URL��
|
956
|
-
* ((<URL:http://www.genome.jp/dbget-bin/www_linkdb>)) (Single entry to database)
|
957
|
-
|
958
|
-
--- get_linkdb_between_databases(string:from_db, string:to_db, int:offset, int:limit)
|
959
|
-
|
960
|
-
���ꤷ�����ĤΥǡ����١����ǡ�����ȥ�֤Υ�����Ƹ������ޤ���
|
961
|
-
|
962
|
-
���͡�
|
963
|
-
ArrayOfLinkDBRelation
|
964
|
-
|
965
|
-
�㡧
|
966
|
-
# ��IJ�ݤ� KEGG GENES �� KEGG PATHWAY �δ֤Υ�����Ƹ���
|
967
|
-
get_linkdb_between_databases("eco", "pathway", 1, 100)
|
968
|
-
|
969
|
-
# Ruby �Ǽ�������������ɽ��������
|
970
|
-
links = get_linkdb_between_databases("eco", "pathway", 1, 100)
|
971
|
-
links.each do |link|
|
972
|
-
puts link.entry_id1 # => "eco:b0084"
|
973
|
-
puts link.entry_id2 # => "path:map00550"
|
974
|
-
puts link.type # => "indirect"
|
975
|
-
puts link.path # => "eco->ec->path"
|
976
|
-
end
|
977
|
-
|
978
|
-
��Ϣ URL��
|
979
|
-
* ((<URL:http://www.genome.jp/dbget-bin/www_linkdb>)) (Database to database)
|
980
|
-
|
981
|
-
+ �����Ҥȹ����ֹ�δط�
|
982
|
-
|
983
|
-
--- get_genes_by_enzyme(string:enzyme_id, string:org)
|
984
|
-
|
985
|
-
�о���ʪ��ˤ����ơ����ꤷ�������ֹ����İ����ҤΥꥹ�Ȥ��֤��ޤ���
|
986
|
-
|
987
|
-
���͡�
|
988
|
-
ArrayOfstring (genes_id)
|
989
|
-
|
990
|
-
�㡧
|
991
|
-
# �����ֹ� 1.1.1.1 �������IJ�ݤΰ����ҤΥꥹ��
|
992
|
-
get_genes_by_enzyme('ec:1.1.1.1', 'eco')
|
993
|
-
|
994
|
-
--- get_enzymes_by_gene(string:genes_id)
|
995
|
-
|
996
|
-
���ꤷ�������Ҥ��б���������ֹ�Υꥹ�Ȥ��֤��ޤ���
|
997
|
-
|
998
|
-
���͡�
|
999
|
-
ArrayOfstring (enzyme_id)
|
1000
|
-
|
1001
|
-
�㡧
|
1002
|
-
# ��IJ�ݰ����� 'eco:b0002' �ι����ֹ�Υꥹ��
|
1003
|
-
get_enzymes_by_gene(eco:b0002)
|
1004
|
-
|
1005
|
-
+ ���ǡ�����ʪ���ꥢ�������δط�
|
1006
|
-
|
1007
|
-
--- get_enzymes_by_compound(string:compound_id)
|
1008
|
-
|
1009
|
-
���ꤷ������ʪ���б���������ֹ�Υꥹ�Ȥ��֤��ޤ���
|
1010
|
-
|
1011
|
-
���͡�
|
1012
|
-
ArrayOfstring (compound_id)
|
1013
|
-
|
1014
|
-
�㡧
|
1015
|
-
# ����ʪ 'cpd:C00345' ����դ˴ؤ����ǤΥꥹ��
|
1016
|
-
get_enzymes_by_compound('cpd:C00345')
|
1017
|
-
|
1018
|
-
--- get_enzymes_by_glycan(string:compound_id)
|
1019
|
-
|
1020
|
-
���ꤷ���������б���������ֹ�Υꥹ�Ȥ��֤��ޤ���
|
1021
|
-
|
1022
|
-
���͡�
|
1023
|
-
ArrayOfstring (glycan_id)
|
1024
|
-
|
1025
|
-
�㡧
|
1026
|
-
# ���� 'gl:G00001' ����դ˴ؤ����ǤΥꥹ��
|
1027
|
-
get_enzymes_by_glycan('gl:G00001')
|
1028
|
-
|
1029
|
-
--- get_enzymes_by_reaction(string:reaction_id)
|
1030
|
-
|
1031
|
-
���ꤷ���ꥢ��������ֹ���б���������ֹ�Υꥹ�Ȥ��֤��ޤ���
|
1032
|
-
|
1033
|
-
���͡�
|
1034
|
-
ArrayOfstring (reaction_id)
|
1035
|
-
|
1036
|
-
�㡧
|
1037
|
-
# �ꥢ��������ֹ� R00100 ����Ĺ��ǤΥꥹ��
|
1038
|
-
get_enzymes_by_reaction('rn:R00100')
|
1039
|
-
|
1040
|
-
--- get_compounds_by_enzyme(string:enzyme_id)
|
1041
|
-
|
1042
|
-
���ꤷ�������ֹ���б����벽��ʪ�Υꥹ�Ȥ��֤��ޤ���
|
1043
|
-
|
1044
|
-
���͡�
|
1045
|
-
ArrayOfstring (compound_id)
|
1046
|
-
|
1047
|
-
�㡧
|
1048
|
-
# �����ֹ� 'ec:2.7.1.12' ����դ˴ؤ�벽��ʪ�Υꥹ��
|
1049
|
-
get_compounds_by_enzyme('ec:2.7.1.12')
|
1050
|
-
|
1051
|
-
--- get_compounds_by_reaction(string:reaction_id)
|
1052
|
-
|
1053
|
-
���ꤷ���ꥢ���������б����벽��ʪ�Υꥹ�Ȥ��֤��ޤ���
|
1054
|
-
|
1055
|
-
���͡�
|
1056
|
-
ArrayOfstring (compound_id)
|
1057
|
-
|
1058
|
-
�㡧
|
1059
|
-
# �ꥢ��������ֹ� 'rn:R00100' ��ȿ���˴ؤ�벽��ʪ�Υꥹ��
|
1060
|
-
get_compounds_by_reaction('rn:R00100')
|
1061
|
-
|
1062
|
-
--- get_glycans_by_enzyme(string:enzyme_id)
|
1063
|
-
|
1064
|
-
���ꤷ�������ֹ���б����������Υꥹ�Ȥ��֤��ޤ���
|
1065
|
-
|
1066
|
-
���͡�
|
1067
|
-
ArrayOfstring (glycan_id)
|
1068
|
-
|
1069
|
-
�㡧
|
1070
|
-
# �����ֹ� 'ec:2.4.1.141' ����դ˴ؤ�������Υꥹ��
|
1071
|
-
get_glycans_by_enzyme('ec:2.4.1.141')
|
1072
|
-
|
1073
|
-
--- get_glycans_by_reaction(string:reaction_id)
|
1074
|
-
|
1075
|
-
���ꤷ���ꥢ���������б����������Υꥹ�Ȥ��֤��ޤ���
|
1076
|
-
|
1077
|
-
���͡�
|
1078
|
-
ArrayOfstring (glycan_id)
|
1079
|
-
|
1080
|
-
�㡧
|
1081
|
-
# �ꥢ��������ֹ� 'rn:R06164' ��ȿ���˴ؤ�������Υꥹ��
|
1082
|
-
get_glycans_by_reaction('rn:R06164')
|
1083
|
-
|
1084
|
-
--- get_reactions_by_enzyme(string:enzyme_id)
|
1085
|
-
|
1086
|
-
���ꤷ�������ֹ���б�����ꥢ�������Υꥹ�Ȥ��֤��ޤ���
|
1087
|
-
|
1088
|
-
���͡�
|
1089
|
-
ArrayOfstring (reaction_id)
|
1090
|
-
|
1091
|
-
�㡧
|
1092
|
-
# �����ֹ� 'ec:2.7.1.12' ��ȿ���˴ؤ��ꥢ��������ֹ�Υꥹ��
|
1093
|
-
get_reactions_by_enzyme('ec:2.7.1.12')
|
1094
|
-
|
1095
|
-
--- get_reactions_by_compound(string:compound_id)
|
1096
|
-
|
1097
|
-
���ꤷ������ʪ���б�����ꥢ�������Υꥹ�Ȥ��֤��ޤ���
|
1098
|
-
|
1099
|
-
���͡�
|
1100
|
-
ArrayOfstring (reaction_id)
|
1101
|
-
|
1102
|
-
�㡧
|
1103
|
-
# ����ʪ 'cpd:C00199' �ο���ȿ���˴ؤ��ꥢ��������ֹ�Υꥹ��
|
1104
|
-
get_reactions_by_compound('cpd:C00199')
|
1105
|
-
|
1106
|
-
--- get_reactions_by_glycan(string:glycan_id)
|
1107
|
-
|
1108
|
-
���ꤷ���������б�����ꥢ�������Υꥹ�Ȥ��֤��ޤ���
|
1109
|
-
|
1110
|
-
���͡�
|
1111
|
-
ArrayOfstring (reaction_id)
|
1112
|
-
|
1113
|
-
�㡧
|
1114
|
-
# ���� 'gl:G00001' �ο���ȿ���˴ؤ��ꥢ��������ֹ�Υꥹ��
|
1115
|
-
get_reactions_by_glycan('gl:G00001')
|
1116
|
-
|
1117
|
-
==== SSDB
|
1118
|
-
|
1119
|
-
SSDB �ǡ����١������Ф����åɤΰ����Ǥ���SSDB �� KEGG/GENES �˴ޤޤ��
|
1120
|
-
����ʪ��������Ҵ֤� ssearch ���Ѥ��� Smith-Waterman ���르�ꥺ���
|
1121
|
-
��븡����Ԥä���̤ȡ��������ҤΥ�����ո�����̤���Ͽ�����ǡ����١����ǡ�
|
1122
|
-
���֤Τ�����������餫���Ὢ��äƤ��뤿���®�ʸ�������ǽ�ˤʤäƤ��ޤ���
|
1123
|
-
|
1124
|
-
KEGG �����Υ�����η�ޤä���ʪ����濴���оݤȤ��Ƥ��뤳�Ȥȡ�Smith-
|
1125
|
-
Waterman �������ˤ����Ӥ��Ǥ��뤳�Ȥ��饪����������ѥ�����ط��ˤ���
|
1126
|
-
�����Ҥ�õ������ʪ���ͭ�ΰ����Ҥθ�����Ϥ����͡��ʱ��Ѥ��ͤ����ޤ���
|
1127
|
-
|
1128
|
-
SSDB �ǡ����١����ˤĤ��ƾܤ����ϰʲ��Υڡ����Ȥ��Ƥ���������
|
1129
|
-
|
1130
|
-
* ((<URL:http://www.genome.jp/kegg/ssdb/>))
|
1131
|
-
|
1132
|
-
|
1133
|
-
--- get_best_best_neighbors_by_gene(string:genes_id, int:offset, int:limit)
|
1134
|
-
|
1135
|
-
������ȥ������åȤ� best-best �δط��ˤ�������Ҥ��������ޤ���
|
1136
|
-
|
1137
|
-
���͡�
|
1138
|
-
ArrayOfSSDBRelation
|
1139
|
-
|
1140
|
-
�㡧
|
1141
|
-
# ��IJ�ݤΰ����� b0002 ��������ʪ��� best-best �δط��ˤ��������
|
1142
|
-
get_best_best_neighbors_by_gene('eco:b0002', 1, 10)
|
1143
|
-
get_best_best_neighbors_by_gene('eco:b0002', 11, 10)
|
1144
|
-
|
1145
|
-
--- get_best_neighbors_by_gene(string:genes_id, int:offset, int:limit)
|
1146
|
-
|
1147
|
-
�����꤫�鸫�ƥ٥��ȥҥåȤδط��ˤ�������Ҥ��������ޤ���
|
1148
|
-
|
1149
|
-
���͡�
|
1150
|
-
ArrayOfSSDBRelation
|
1151
|
-
|
1152
|
-
�㡧
|
1153
|
-
# ��IJ�ݤΰ����� b0002 ��������ʪ��� best neighbor �δط��ˤ��������
|
1154
|
-
get_best_neighbors_by_gene('eco:b0002', 1, 10)
|
1155
|
-
get_best_neighbors_by_gene('eco:b0002', 11, 10)
|
1156
|
-
|
1157
|
-
--- get_reverse_best_neighbors_by_gene(string:genes_id, int:offset, int:limit)
|
1158
|
-
|
1159
|
-
�������å�¦����ʪ�狼�鸫�ƥ����꤬�٥��ȥҥåȤȤʤ�����Ҥ����ޤ���
|
1160
|
-
|
1161
|
-
���͡�
|
1162
|
-
ArrayOfSSDBRelation
|
1163
|
-
|
1164
|
-
�㡧
|
1165
|
-
# ��IJ�ݤΰ����� b0002 �� reverse best neighbor �δط��ˤ��������
|
1166
|
-
get_reverse_best_neighbors_by_gene('eco:b0002', 1, 10)
|
1167
|
-
get_reverse_best_neighbors_by_gene('eco:b0002', 11, 10)
|
1168
|
-
|
1169
|
-
--- get_paralogs_by_gene(string:genes_id, int:offset, int:limit)
|
1170
|
-
|
1171
|
-
�������Ʊ����ʪ����ǥѥ���������Ҥ����ޤ���
|
1172
|
-
|
1173
|
-
���͡�
|
1174
|
-
ArrayOfSSDBRelation
|
1175
|
-
|
1176
|
-
�㡧
|
1177
|
-
# ��IJ�ݤΰ����� b0002 �ȥѥ�����δط��ˤ��������
|
1178
|
-
get_paralogs_by_gene('eco:b0002', 1, 10)
|
1179
|
-
get_paralogs_by_gene('eco:b0002', 11, 10)
|
1180
|
-
|
1181
|
-
|
1182
|
-
==== Motif
|
1183
|
-
|
1184
|
-
--- get_motifs_by_gene(string:genes_id, string:db)
|
1185
|
-
|
1186
|
-
���ꤷ�������Ҥ�¸�ߤ��������դΥꥹ�Ȥ��֤��ޤ���������եǡ����١���
|
1187
|
-
�Υꥹ�Ȥˤϡ�Pfam (pfam), TIGRFAM (tfam), PROSITE pattern (pspt), PROSITE
|
1188
|
-
profile (pspf) �ޤ��Ϥ�������� (all) ��������ޤ���
|
1189
|
-
|
1190
|
-
���͡�
|
1191
|
-
ArrayOfMotifResult
|
1192
|
-
|
1193
|
-
�㡧
|
1194
|
-
# ��IJ�ݤΰ����� b0002 ����Pfam������դΥꥹ��
|
1195
|
-
get_motifs_by_gene('eco:b0002', 'pfam')
|
1196
|
-
|
1197
|
-
--- get_genes_by_motifs([string]:motif_id_list, int:offset, int:limit)
|
1198
|
-
|
1199
|
-
���ꤷ��������դ����ƻ��İ����Ҥ����ޤ���
|
1200
|
-
|
1201
|
-
���͡�
|
1202
|
-
ArrayOfDefinition (genes_id, definition)
|
1203
|
-
|
1204
|
-
�㡧
|
1205
|
-
# Pfam �� DnaJ �� Prosite �� DNAJ_2 �˥ҥåȤ�������Ҥ�
|
1206
|
-
list = ['pf:DnaJ', 'ps:DNAJ_2']
|
1207
|
-
get_genes_by_motifs(list, 1, 10)
|
1208
|
-
get_genes_by_motifs(list, 11, 10)
|
1209
|
-
|
1210
|
-
==== KO
|
1211
|
-
|
1212
|
-
KO (KEGG orthology), OC (KEGG ortholog cluster), PC (KEGG paralog cluster) ��
|
1213
|
-
��������뤿��Υ�åɤǤ���KO �ϥ���졼����줿���������������ҷ���
|
1214
|
-
OC �� PC �ϵ���Ū�˥��饹������줿��Ʊ���Τ�������ҷ��Υǡ����١����Ǥ���
|
1215
|
-
|
1216
|
-
--- get_ko_by_gene(string:genes_id)
|
1217
|
-
|
1218
|
-
���ꤷ�������Ҥ˥�������Ƥ��� KO �Υ���ȥ��ֹ�������֤��ޤ���
|
1219
|
-
|
1220
|
-
���͡�
|
1221
|
-
ArrayOfstring (ko_id)
|
1222
|
-
|
1223
|
-
�㡧
|
1224
|
-
# eco:b0002 �����Ҥ˥�������Ƥ��� KO �Υꥹ��
|
1225
|
-
get_ko_by_gene('eco:b0002')
|
1226
|
-
|
1227
|
-
|
1228
|
-
--- get_ko_by_ko_class(string:ko_class_id)
|
1229
|
-
|
1230
|
-
���ꤷ�� ko_class_id �˴ޤޤ�� ko_id �Υꥹ�Ȥ��֤��ޤ���
|
1231
|
-
|
1232
|
-
���͡�
|
1233
|
-
ArrayOfDefinition (ko_id)
|
1234
|
-
|
1235
|
-
�㡧
|
1236
|
-
# KO class '01196' �˴ޤޤ�� KO �Υꥹ��
|
1237
|
-
get_ko_by_ko_class('01196')
|
1238
|
-
|
1239
|
-
--- get_genes_by_ko_class(string:ko_class_id, string:org, int:offset, int:limit)
|
1240
|
-
|
1241
|
-
���ꤷ����ʪ��� ko_class_id �˴ޤޤ������ҤΥꥹ�Ȥ��֤��ޤ���
|
1242
|
-
|
1243
|
-
���͡�
|
1244
|
-
ArrayOfDefinition (genes_id, definition)
|
1245
|
-
|
1246
|
-
�㡧
|
1247
|
-
# KO ���饹 '00930' �˴ޤޤ��ҥȰ����ҤΥꥹ��
|
1248
|
-
get_genes_by_ko_class('00903', 'hsa' , 1, 100)
|
1249
|
-
|
1250
|
-
--- get_genes_by_ko(string:ko_id, string:org)
|
1251
|
-
|
1252
|
-
���ꤷ����ʪ��� ko_id �˴ޤޤ������ҤΥꥹ�Ȥ��֤��ޤ���
|
1253
|
-
��ʪ�拾���ɤ� all ����ꤹ�������ʪ��ΰ����Ҥ��֤��ޤ���
|
1254
|
-
|
1255
|
-
���͡�
|
1256
|
-
ArrayOfDefinition (genes_id, definition)
|
1257
|
-
|
1258
|
-
�㡧
|
1259
|
-
# KO �ֹ� 'K00001' �˴ޤޤ����IJ�ݰ����ҤΥꥹ��
|
1260
|
-
get_genes_by_ko('ko:K00010', 'eco')
|
1261
|
-
|
1262
|
-
# KO �ֹ� 'K00010' �˴ޤޤ������ʪ��ΰ����ҥꥹ��
|
1263
|
-
get_genes_by_ko('ko:K00010', 'all')
|
1264
|
-
|
1265
|
-
|
1266
|
-
|
1267
|
-
==== PATHWAY
|
1268
|
-
|
1269
|
-
PATHWAY �ǡ����١������Ф����åɤΰ����Ǥ���PATHWAY �ǡ����١�����
|
1270
|
-
�Ĥ��ƾܤ����ϰʲ��Υڡ����Ȥ��Ƥ���������
|
1271
|
-
|
1272
|
-
* ((<URL:http://www.genome.jp/kegg/kegg2.html#pathway>))
|
1273
|
-
|
1274
|
-
+ �ѥ��������ؤο��Ť�
|
1275
|
-
|
1276
|
-
��Ϣ URL��
|
1277
|
-
* ((<URL:http://www.genome.jp/kegg/tool/color_pathway.html>))
|
1278
|
-
|
1279
|
-
--- mark_pathway_by_objects(string:pathway_id, [string]:object_id_list)
|
1280
|
-
|
1281
|
-
���ꤷ����ʪ��ǡ�Ϳ����줿�ѥ��������ޥåפ�Ϳ����줿���֥�������
|
1282
|
-
�ʰ����ҡ�����ʪ�������ֹ�ˤ��б������Ȥ˿���Ĥ���������������
|
1283
|
-
������ URL ���֤��ޤ���
|
1284
|
-
|
1285
|
-
���͡�
|
1286
|
-
string (URL)
|
1287
|
-
|
1288
|
-
�㡧
|
1289
|
-
# ��IJ�ݤΥѥ������� path:eco00260 ��ΰ����� eco:b0002 �� Homoserine
|
1290
|
-
# �� cpd:C00263 ���б�����ܥå������֤��忧���������� URL
|
1291
|
-
obj_list = ['eco:b0002', 'cpd:C00263']
|
1292
|
-
mark_pathway_by_objects('path:eco00260', obj_list)
|
1293
|
-
|
1294
|
-
--- color_pathway_by_objects(string:pathway_id, [string]:object_id_list, [string]:fg_color_list, [string]:bg_color_list)
|
1295
|
-
|
1296
|
-
���ꤷ���ѥ���������Ϳ����줿���֥������ȡʰ����ҡ�����ʪ�����ǡˤ��Ф���
|
1297
|
-
ʸ�����Ȥ� fg_color_list �ǻ��ꤷ�������طʤ� bg_color_list �ǻ��ꤷ������
|
1298
|
-
�Ĥ��������������������� URL ���֤��ޤ���object_id_list �� fg_color_list,
|
1299
|
-
bg_color_list �����Ǥο��Ƚ��֤�·����褦�����դ���ɬ�פ�����ޤ���
|
1300
|
-
|
1301
|
-
���͡�
|
1302
|
-
string (URL)
|
1303
|
-
|
1304
|
-
�㡧
|
1305
|
-
# �ѥ������� path:eco00053 ��˺ܤäƤ�����IJ�ݤΰ����� eco:b0207 ��
|
1306
|
-
# �طʤ��֡�ʸ�����Ȥ��Ĥ��忧����eco:b1300 ���طʤ���ʸ�����Ȥ��Ф�
|
1307
|
-
# �忧���������� URL ���֤��ޤ���
|
1308
|
-
obj_list = ['eco:b0207', 'eco:b1300']
|
1309
|
-
fg_list = ['blue', '#00ff00']
|
1310
|
-
bg_list = ['#ff0000', 'yellow']
|
1311
|
-
color_pathway_by_objects('path:eco00053', obj_list, fg_list, bg_list)
|
1312
|
-
|
1313
|
-
--- color_pathway_by_elements(string:pathway_id, [int]:element_id_list, [string]:fg_color_list, [string]:bg_color_list)
|
1314
|
-
|
1315
|
-
���ꤷ�� element_id ���б�����ѥ���������Υ��֥������ȡ�Ĺ������ݤʤɡ�
|
1316
|
-
���Ф���ʸ�����Ȥ� fg_color_list �ǻ��ꤷ�������طʤ� bg_color_list ��
|
1317
|
-
���ꤷ������Ĥ��������������������� URL ���֤��ޤ���object_id_list ��
|
1318
|
-
fg_color_list, bg_color_list �����Ǥο��Ƚ��֤�·����褦�����դ���
|
1319
|
-
ɬ�פ�����ޤ���
|
1320
|
-
|
1321
|
-
KEGG PATHWAY �Ǥϡ�ʣ���ΰ����Ҥ���ĤΥܥå����˳�����Ƥ��Ƥ����ꡢ
|
1322
|
-
�դˣ��Ĥΰ����Ҥ�ʣ���Υܥå����˳�����Ƥ��Ƥ��뤳�Ȥ�����ޤ���
|
1323
|
-
���Τ褦�ʾ�� color_pathway_by_objects ��åɤǤ��ɤ�ʬ���뤳�Ȥ�
|
1324
|
-
����ޤ���color_pathway_by_elements ��Ȥ����ȤDz��Ǥ��ޤ���
|
1325
|
-
|
1326
|
-
element_id �� KEGG PATHWAY �� XML ɽ���Ǥ��� KGML �� <entry> ������
|
1327
|
-
���ꤵ��롢�ѥ���������Υ���ե������������ˤĤ���줿��ˡ�����
|
1328
|
-
���ͤǤ����ѥ���������� element_id �� get_elements_by_pathway ��åɤ�
|
1329
|
-
PathwayElement ���֥������ȤΥꥹ�ȤȤ������뤳�Ȥ��Ǥ��ޤ���
|
1330
|
-
PathwayElement �� type �� name °���ˤ������ҡ����ǡ�����ʪ�ʤɤ�
|
1331
|
-
�б����ꡢelement_id ���ͤ�Ȥäƥ��֥������Ȥ����ꤷ�ޤ���
|
1332
|
-
|
1333
|
-
KGML �ˤĤ��ƾܤ����ϲ����Υڡ����Ȥ��Ƥ���������
|
1334
|
-
|
1335
|
-
* ((<URL:http://www.genome.jp/kegg/xml/>))
|
1336
|
-
|
1337
|
-
����͡�
|
1338
|
-
string (URL)
|
1339
|
-
|
1340
|
-
�㡧
|
1341
|
-
# ����ݤΥѥ������� path:bsu00010 ��˺ܤäƤ��롢
|
1342
|
-
# ������ bsu:BG11350 (element_id 78, ec:3.2.1.86) ������/���طʤ�
|
1343
|
-
# ������ bsu:BG11203 (element_id 79, ec:3.2.1.86) ������/���طʤ�
|
1344
|
-
# ������ bsu:BG11685 (element_id 51, ec:2.7.1.2) ������/���طʤ�
|
1345
|
-
# ������ bsu:BG11685 (element_id 47, ec:2.7.1.2) ������/���طʤ�
|
1346
|
-
# ���줾���忧���������� URL ���֤��ޤ���
|
1347
|
-
element_id_list = [ 78, 79, 51, 47 ]
|
1348
|
-
fg_list = [ '#ff0000', '#0000ff', '#ff0000', '#0000ff' ]
|
1349
|
-
bg_list = [ '#ffff00', '#ffff00', '#ffcc00', '#ffcc00' ]
|
1350
|
-
color_pathway_by_elements('path:bsu00010', element_id_list, fg_list, bg_list)
|
1351
|
-
|
1352
|
-
--- get_html_of_marked_pathway_by_objects(string:pathway_id, [string]:object_id_list)
|
1353
|
-
|
1354
|
-
����������˥���å��֥�ޥåפ�ޤ� HTML �ڡ����� URL ���֤�
|
1355
|
-
�С������� 'mark_pathway_by_objects' ��åɤǤ���
|
1356
|
-
|
1357
|
-
���͡�
|
1358
|
-
string (URL)
|
1359
|
-
|
1360
|
-
�㡧
|
1361
|
-
# ��IJ�ݤΥѥ������� '00970' �Ρ������� 'eco:b4258'������ʪ 'cpd:C00135'
|
1362
|
-
# KO �ֹ� 'ko:K01881' ���ֿ��ǥޡ�����Ĥ��������Υ���å��֥�ޥåפ�
|
1363
|
-
# ɽ������ HTML �� URL ���֤�
|
1364
|
-
obj_list = ['eco:b4258', 'cpd:C00135', 'ko:K01881']
|
1365
|
-
get_html_of_marked_pathway_by_objects('path:eco00970', obj_list)
|
1366
|
-
|
1367
|
-
--- get_html_of_colored_pathway_by_objects(string:pathway_id, [string]:object_id_list, [string]:fg_color_list, [string]:bg_color_list)
|
1368
|
-
|
1369
|
-
����������˥���å��֥�ޥåפ�ޤ� HTML �ڡ����� URL ���֤�
|
1370
|
-
�С������� 'color_pathway_by_objects' ��åɤǤ���
|
1371
|
-
|
1372
|
-
���͡�
|
1373
|
-
string (URL)
|
1374
|
-
|
1375
|
-
�㡧
|
1376
|
-
# ��IJ�ݤΥѥ������� '00970' �Ρ������� 'eco:b4258' �����Ϥ˳���������ʪ
|
1377
|
-
# 'cpd:C00135' ���Ϥ��С�KO �ֹ� 'ko:K01881' �����Ϥ��Ĥο��Ť���
|
1378
|
-
# �����Υ���å��֥�ޥåפ�ɽ������ HTML �� URL ���֤�
|
1379
|
-
obj_list = ['eco:b4258', 'cpd:C00135', 'ko:K01881']
|
1380
|
-
fg_list = ['gray', '#00ff00', 'blue']
|
1381
|
-
bg_list = ['#ff0000', 'yellow', 'orange']
|
1382
|
-
get_html_of_colored_pathway_by_objects('path:eco00970', obj_list, fg_list, bg_list)
|
1383
|
-
|
1384
|
-
--- get_html_of_colored_pathway_by_elements(string:pathway_id, [int]:element_id_list, [string]:fg_color_list, [string]:bg_color_list)
|
1385
|
-
|
1386
|
-
����������˥���å��֥�ޥåפ�ޤ� HTML �ڡ����� URL ���֤�
|
1387
|
-
�С������� 'color_pathway_by_elements' ��åɤǤ���
|
1388
|
-
|
1389
|
-
���͡�
|
1390
|
-
string (URL)
|
1391
|
-
|
1392
|
-
�㡧
|
1393
|
-
# ����ݤΥѥ������� path:bsu00010 ��˺ܤäƤ��롢
|
1394
|
-
# ������ bsu:BG11350 (element_id 78, ec:3.2.1.86) ������/���طʤ�
|
1395
|
-
# ������ bsu:BG11203 (element_id 79, ec:3.2.1.86) ������/���طʤ�
|
1396
|
-
# ������ bsu:BG11685 (element_id 51, ec:2.7.1.2) ������/���طʤ�
|
1397
|
-
# ������ bsu:BG11685 (element_id 47, ec:2.7.1.2) ������/���طʤ�
|
1398
|
-
# �忧���������Υ���å��֥�ޥåפ�ɽ������ HTML �� URL ���֤��ޤ���
|
1399
|
-
element_id_list = [ 78, 79, 51, 47 ]
|
1400
|
-
fg_list = [ '#ff0000', '#0000ff', '#ff0000', '#0000ff' ]
|
1401
|
-
bg_list = [ '#ffff00', '#ffff00', '#ffcc00', '#ffcc00' ]
|
1402
|
-
color_pathway_by_elements('path:bsu00010', element_id_list, fg_list, bg_list)
|
1403
|
-
|
1404
|
-
+ �ѥ���������Υ��֥������ȴ֤δط�
|
1405
|
-
|
1406
|
-
--- get_element_relations_by_pathway(string:pathway_id)
|
1407
|
-
|
1408
|
-
���ꤷ���ѥ���������˺ܤäƤ��륪�֥����������Ǥδ֤δط����֤��ޤ���
|
1409
|
-
�ѥ��������������ˤ��������Ƥ���ط���ɽ����KGML �ˤ�����
|
1410
|
-
<relation> �������������ʥ���աˤ�������뤳�Ȥ��Ǥ��ޤ���
|
1411
|
-
���� get_elements_by_pathway ��åɤ⻲�ȡ�
|
1412
|
-
|
1413
|
-
���͡�
|
1414
|
-
ArrayOfPathwayElementRelation
|
1415
|
-
|
1416
|
-
�㡧
|
1417
|
-
# ����ݤΥѥ������� path:bsu00010 ��˺ܤäƤ��� PathwayElement �֤�
|
1418
|
-
# �ط��Ǥ��� PathwayElementRelation �Υꥹ�Ȥ�������롣
|
1419
|
-
relations = get_element_relations_by_pathway('path:bsu00010')
|
1420
|
-
|
1421
|
-
# ���������ꥹ�Ȥ���Ȥ�ɽ�����롣
|
1422
|
-
relations.each do |rel|
|
1423
|
-
puts rel.element_id1
|
1424
|
-
puts rel.element_id2
|
1425
|
-
puts rel.type
|
1426
|
-
rel.subtypes.each do |sub|
|
1427
|
-
puts sub.element_id
|
1428
|
-
puts sub.relation
|
1429
|
-
puts sub.type
|
1430
|
-
end
|
1431
|
-
end
|
1432
|
-
|
1433
|
-
+ �ѥ���������Υ��֥������ȸ���
|
1434
|
-
|
1435
|
-
--- get_elements_by_pathway(string:pathway_id)
|
1436
|
-
|
1437
|
-
���ꤷ���ѥ���������˺ܤäƤ��륪�֥����������ǤΥꥹ�Ȥ��֤��ޤ���
|
1438
|
-
����ˡ�ˤĤ��Ƥ� color_pathway_by_elements ��åɤȤ��Ƥ���������
|
1439
|
-
|
1440
|
-
���͡�
|
1441
|
-
ArrayOfPathwayElement
|
1442
|
-
|
1443
|
-
�㡧
|
1444
|
-
# ����ݤΥѥ������� path:bsu00010 ��˺ܤäƤ��� PathwayElement ��
|
1445
|
-
# �ꥹ�Ȥ�������롣
|
1446
|
-
get_elements_by_pathway('path:bsu00010')
|
1447
|
-
|
1448
|
-
# Ruby �ǰ����� bsu:BG11350, bsu:BG11203 �� bsu:BG11685 �� element_id ��
|
1449
|
-
# Ĵ�٤��㡣
|
1450
|
-
elems = serv.get_elements_by_pathway('path:bsu00010')
|
1451
|
-
genes = [ 'bsu:BG11350', 'bsu:BG11203', 'bsu:BG11685' ]
|
1452
|
-
elems.each do |elem|
|
1453
|
-
genes.each do |gene|
|
1454
|
-
if elem.names.include?(gene)
|
1455
|
-
puts gene, elem.element_id
|
1456
|
-
end
|
1457
|
-
end
|
1458
|
-
end
|
1459
|
-
|
1460
|
-
--- get_genes_by_pathway(string:pathway_id)
|
1461
|
-
|
1462
|
-
���ꤷ���ѥ���������˺ܤäƤ�������ҤΥꥹ�Ȥ��֤��ޤ�����ʪ��̾��
|
1463
|
-
pathway_id �˴ޤޤ�� keggorg �ǻ��ꤷ�ޤ���
|
1464
|
-
|
1465
|
-
���͡�
|
1466
|
-
ArrayOfstring (genes_id)
|
1467
|
-
|
1468
|
-
�㡧
|
1469
|
-
# ��IJ�ݤΥѥ������� 00020 �֤˺ܤäƤ�������ҤΥꥹ��
|
1470
|
-
get_genes_by_pathway('path:eco00020')
|
1471
|
-
|
1472
|
-
--- get_enzymes_by_pathway(string:pathway_id)
|
1473
|
-
|
1474
|
-
���ꤷ���ѥ��������˺ܤäƤ�������ֹ�Υꥹ�Ȥ��֤��ޤ���
|
1475
|
-
|
1476
|
-
���͡�
|
1477
|
-
ArrayOfstring (enzyme_id)
|
1478
|
-
|
1479
|
-
�㡧
|
1480
|
-
# ��IJ�ݤΥѥ������� 00020 �֤˺ܤäƤ�������ֹ�Υꥹ��
|
1481
|
-
get_enzymes_by_pathway('path:eco00020')
|
1482
|
-
|
1483
|
-
--- get_compounds_by_pathway(string:pathway_id)
|
1484
|
-
|
1485
|
-
���ꤷ���ѥ��������˺ܤäƤ��벽��ʪ�Υꥹ�Ȥ��֤��ޤ���
|
1486
|
-
|
1487
|
-
���͡�
|
1488
|
-
ArrayOfstring (compound_id)
|
1489
|
-
|
1490
|
-
�㡧
|
1491
|
-
# ��IJ�ݤΥѥ������� 00020 �˺ܤäƤ��벽��ʪ�Υꥹ��
|
1492
|
-
get_compounds_by_pathway('path:eco00020')
|
1493
|
-
|
1494
|
-
--- get_glycans_by_pathway(string:pathway_id)
|
1495
|
-
|
1496
|
-
���ꤷ���ѥ��������˺ܤäƤ��������Υꥹ�Ȥ��֤��ޤ���
|
1497
|
-
|
1498
|
-
���͡�
|
1499
|
-
ArrayOfstring (glycan_id)
|
1500
|
-
|
1501
|
-
�㡧
|
1502
|
-
# ��IJ�ݤΥѥ������� 00510 �˺ܤäƤ��������Υꥹ��
|
1503
|
-
get_glycans_by_pathway('path:eco00510')
|
1504
|
-
|
1505
|
-
--- get_reactions_by_pathway(string:pathway_id)
|
1506
|
-
|
1507
|
-
���ꤷ���ѥ��������˺ܤäƤ���ꥢ��������ֹ�Υꥹ�Ȥ��֤��ޤ���
|
1508
|
-
|
1509
|
-
���͡�
|
1510
|
-
ArrayOfstring (reaction_id)
|
1511
|
-
|
1512
|
-
�㡧
|
1513
|
-
# ��IJ�ݤΥѥ������� 00260 �֤˺ܤäƤ���ꥢ�������Υꥹ��
|
1514
|
-
get_reactions_by_pathway('path:eco00260')
|
1515
|
-
|
1516
|
-
--- get_kos_by_pathway(string:pathway_id)
|
1517
|
-
|
1518
|
-
���ꤷ���ѥ��������˺ܤäƤ��� KO �ֹ�Υꥹ�Ȥ��֤��ޤ���
|
1519
|
-
|
1520
|
-
���͡�
|
1521
|
-
ArrayOfstring (ko_id)
|
1522
|
-
|
1523
|
-
�㡧
|
1524
|
-
# �ҥȤΥѥ������� 00010 �˺ܤäƤ��� KO �ֹ�Υꥹ��
|
1525
|
-
get_kos_by_pathway('path:hsa00010')
|
1526
|
-
|
1527
|
-
+ ���֥������Ȥ���ѥ�����������
|
1528
|
-
|
1529
|
-
��Ϣ URL��
|
1530
|
-
* ((<URL:http://www.genome.jp/kegg/tool/search_pathway.html>))
|
1531
|
-
|
1532
|
-
--- get_pathways_by_genes([string]:genes_id_list)
|
1533
|
-
|
1534
|
-
���ꤷ�������Ҥ����ƺܤäƤ���ѥ��������Υꥹ�Ȥ��֤��ޤ���
|
1535
|
-
|
1536
|
-
���͡�
|
1537
|
-
ArrayOfstring (pathway_id)
|
1538
|
-
|
1539
|
-
�㡧
|
1540
|
-
# ��IJ�ݤΰ����� b0077 �� b0078 ��ξ���ܤäƤ���ѥ��������Υꥹ��
|
1541
|
-
get_pathways_by_genes(['eco:b0077', 'eco:b0078'])
|
1542
|
-
|
1543
|
-
--- get_pathways_by_enzymes([string]:enzyme_id_list)
|
1544
|
-
|
1545
|
-
���ꤷ�������ֹ椬���ƺܤäƤ���ѥ��������Υꥹ�Ȥ��֤��ޤ���
|
1546
|
-
|
1547
|
-
���͡�
|
1548
|
-
ArrayOfstring (pathway_id)
|
1549
|
-
|
1550
|
-
�㡧
|
1551
|
-
# �����ֹ� 1.3.99.1 �ι��Ǥ��ܤäƤ���ѥ��������Υꥹ��
|
1552
|
-
get_pathways_by_enzymes(['ec:1.3.99.1'])
|
1553
|
-
|
1554
|
-
--- get_pathways_by_compounds([string]:compound_id_list)
|
1555
|
-
|
1556
|
-
���ꤷ������ʪ�����ƺܤäƤ���ѥ��������Υꥹ�Ȥ��֤��ޤ���
|
1557
|
-
|
1558
|
-
���͡�
|
1559
|
-
ArrayOfstring (pathway_id)
|
1560
|
-
|
1561
|
-
�㡧
|
1562
|
-
# ����ʪ C00033 �� C00158 ��ξ���ܤäƤ���ѥ��������Υꥹ��
|
1563
|
-
get_pathways_by_compounds(['cpd:C00033', 'cpd:C00158'])
|
1564
|
-
|
1565
|
-
--- get_pathways_by_glycans([string]:compound_id_list)
|
1566
|
-
|
1567
|
-
���ꤷ�����������ƺܤäƤ���ѥ��������Υꥹ�Ȥ��֤��ޤ���
|
1568
|
-
|
1569
|
-
���͡�
|
1570
|
-
ArrayOfstring (pathway_id)
|
1571
|
-
|
1572
|
-
�㡧
|
1573
|
-
# ���� G00009 �� G00011 ��ξ���ܤäƤ���ѥ��������Υꥹ��
|
1574
|
-
get_pathways_by_glycans(['gl:G00009', 'gl:G00011'])
|
1575
|
-
|
1576
|
-
--- get_pathways_by_reactions([string]:reaction_id_list)
|
1577
|
-
|
1578
|
-
���ꤷ���ꥢ��������ֹ椬���ƺܤäƤ���ѥ��������Υꥹ�Ȥ��֤��ޤ���
|
1579
|
-
|
1580
|
-
���͡�
|
1581
|
-
ArrayOfstring (pathway_id)
|
1582
|
-
|
1583
|
-
�㡧
|
1584
|
-
# �ꥢ��������ֹ� rn:R00959, rn:R02740, rn:R00960, rn:R01786 �����Ƥ�
|
1585
|
-
# ȿ����ޤ�ѥ��������Υꥹ��
|
1586
|
-
get_pathways_by_reactions(['rn:R00959', 'rn:R02740', 'rn:R00960', 'rn:R01786'])
|
1587
|
-
|
1588
|
-
--- get_pathways_by_kos([string]:ko_id_list, string:org)
|
1589
|
-
|
1590
|
-
���ꤷ����ʪ�� KO �ֹ椬���ƺܤäƤ���ѥ��������Υꥹ�Ȥ��֤��ޤ���
|
1591
|
-
|
1592
|
-
���͡�
|
1593
|
-
ArrayOfstring (pathway_id)
|
1594
|
-
|
1595
|
-
�㡧
|
1596
|
-
# KO �ֹ� 'ko:K00016' �� 'ko:K00382' ��ޤ�ҥȤΥѥ��������Υꥹ��
|
1597
|
-
get_pathways_by_kos(['ko:K00016', 'ko:K00382'], 'hsa')
|
1598
|
-
|
1599
|
-
# KO �ֹ� 'ko:K00016' �� 'ko:K00382' ��ޤ�����ʪ��Υѥ��������Υꥹ��
|
1600
|
-
get_pathways_by_kos(['ko:K00016', 'ko:K00382'], 'all')
|
1601
|
-
|
1602
|
-
+ �ѥ��������֤δط�
|
1603
|
-
|
1604
|
-
--- get_linked_pathways(string:pathway_id)
|
1605
|
-
|
1606
|
-
���ꤷ���ѥ��������ֹ�Υѥ���������������Ƥ���ѥ���������
|
1607
|
-
�ꥹ�Ȥ��֤��ޤ���
|
1608
|
-
|
1609
|
-
���͡�
|
1610
|
-
ArrayOfstring (pathway_id)
|
1611
|
-
|
1612
|
-
�㡧
|
1613
|
-
# �ѥ������� path:eco00620 ��������Ƥ���ѥ��������Υꥹ��
|
1614
|
-
get_linked_pathways('path:eco00620')
|
1615
|
-
|
1616
|
-
==== GENES
|
1617
|
-
|
1618
|
-
GENES �ǡ����١������Ф����åɤΰ����Ǥ���GENES �ǡ����١����ˤĤ���
|
1619
|
-
�ܤ����ϰʲ��Υڡ����Ȥ��Ƥ���������
|
1620
|
-
|
1621
|
-
* ((<URL:http://www.genome.jp/kegg/kegg2.html#genes>))
|
1622
|
-
|
1623
|
-
--- get_genes_by_organism(string:org, int:offset, int:limit)
|
1624
|
-
|
1625
|
-
���ꤷ����ʪ����� GENES ����ȥ�Τ�����offset ���ܤ��� limit ʬ��
|
1626
|
-
��̤��֤��ޤ���
|
1627
|
-
|
1628
|
-
���͡�
|
1629
|
-
ArrayOfstring (genes_id)
|
1630
|
-
|
1631
|
-
�㡧
|
1632
|
-
# ����ե륨�ݤΰ����ҥꥹ�Ȥ� 100 �Ĥ�������
|
1633
|
-
get_genes_by_organism('hin', 1, 100)
|
1634
|
-
get_genes_by_organism('hin', 101, 100)
|
1635
|
-
|
1636
|
-
==== GENOME
|
1637
|
-
|
1638
|
-
GENOME �ǡ����١������Ф����åɤΰ����Ǥ���GENOME �ǡ����١����ˤĤ���
|
1639
|
-
�ܤ����ϰʲ��Υڡ����Ȥ��Ƥ���������
|
1640
|
-
|
1641
|
-
* ((<URL:http://www.genome.jp/kegg/kegg2.html#genome>))
|
1642
|
-
|
1643
|
-
--- get_number_of_genes_by_organism(string:org)
|
1644
|
-
|
1645
|
-
���ꤷ����ʪ�郎���İ����ҿ����֤��ޤ���
|
1646
|
-
|
1647
|
-
���͡�
|
1648
|
-
int
|
1649
|
-
|
1650
|
-
�㡧
|
1651
|
-
# ��IJ�ݤ����İ����Ҥο�
|
1652
|
-
get_number_of_genes_by_organism('eco')
|
1653
|
-
|
1654
|
-
==== LIGAND
|
1655
|
-
|
1656
|
-
LIGAND �ǡ����١������Ф����åɤΰ����Ǥ���
|
1657
|
-
|
1658
|
-
��Ϣ URL��
|
1659
|
-
* ((<URL:http://www.genome.jp/kegg/ligand.html>))
|
1660
|
-
|
1661
|
-
--- convert_mol_to_kcf(string:mol)
|
1662
|
-
|
1663
|
-
MOL �ե����ޥåȤΥ���ȥ�� KCF �ե����ޥåȤ��Ѵ����ޤ���
|
1664
|
-
|
1665
|
-
���͡�
|
1666
|
-
string
|
1667
|
-
|
1668
|
-
�㡧
|
1669
|
-
convert_mol_to_kcf(mol_str)
|
1670
|
-
|
1671
|
-
--- search_compounds_by_name(string:name)
|
1672
|
-
|
1673
|
-
����ʪ��̾���Ǹ������ޤ���
|
1674
|
-
|
1675
|
-
���͡�
|
1676
|
-
ArrayOfstring (compound_id)
|
1677
|
-
|
1678
|
-
�㡧
|
1679
|
-
search_compounds_by_name("shikimic acid")
|
1680
|
-
|
1681
|
-
--- search_drugs_by_name(string:name)
|
1682
|
-
|
1683
|
-
�ɥ�å���̾���Ǹ������ޤ���
|
1684
|
-
|
1685
|
-
���͡�
|
1686
|
-
ArrayOfstring (drug_id)
|
1687
|
-
|
1688
|
-
�㡧
|
1689
|
-
search_drugs_by_name("tetracyclin")
|
1690
|
-
|
1691
|
-
--- search_glycans_by_name(string:name)
|
1692
|
-
|
1693
|
-
������̾���Ǹ������ޤ���
|
1694
|
-
|
1695
|
-
���͡�
|
1696
|
-
ArrayOfstring
|
1697
|
-
|
1698
|
-
�㡧
|
1699
|
-
search_glycans_by_name("Paragloboside")
|
1700
|
-
|
1701
|
-
--- search_compounds_by_composition(string:composition)
|
1702
|
-
|
1703
|
-
����ʪ�������Ǹ������ޤ���
|
1704
|
-
�����ϸ��ǤȸĿ���Ĥʤ���ʸ����ǻ��ꤷ�ޤ���
|
1705
|
-
���Ǥν��֤�̵�ط��Ǥ���
|
1706
|
-
|
1707
|
-
���͡�
|
1708
|
-
ArrayOfstring (compound_id)
|
1709
|
-
|
1710
|
-
�㡧
|
1711
|
-
search_compounds_by_composition("C7H10O5")
|
1712
|
-
|
1713
|
-
--- search_drugs_by_composition(string:composition)
|
1714
|
-
|
1715
|
-
�ɥ�å��������Ǹ������ޤ���
|
1716
|
-
�����ϸ��ǤȸĿ���Ĥʤ���ʸ����ǻ��ꤷ�ޤ���
|
1717
|
-
���Ǥν��֤�̵�ط��Ǥ���
|
1718
|
-
|
1719
|
-
���͡�
|
1720
|
-
ArrayOfstring (drug_id)
|
1721
|
-
|
1722
|
-
�㡧
|
1723
|
-
search_drugs_by_composition("HCl")
|
1724
|
-
|
1725
|
-
--- search_glycans_by_composition(string:composition)
|
1726
|
-
|
1727
|
-
�����������Ǹ������ޤ���
|
1728
|
-
�����ϥ��å��dz�ä����ȸĿ��ڡ����Ƕ��ڤä�ʸ����ǻ��ꤷ�ޤ���
|
1729
|
-
���ν��֤ϼ�ͳ�Ǥ���
|
1730
|
-
|
1731
|
-
���͡�
|
1732
|
-
ArrayOfstring
|
1733
|
-
|
1734
|
-
�㡧
|
1735
|
-
search_glycans_by_composition("(Man)4 (GalNAc)1")
|
1736
|
-
|
1737
|
-
--- search_compounds_by_mass(float:mass, float:range)
|
1738
|
-
|
1739
|
-
����ʪ��ʬ���̤Ǹ������ޤ���
|
1740
|
-
mass ���濴�Ȥ��� ��range �νŤ��β���ʪ����������ޤ���
|
1741
|
-
|
1742
|
-
���͡�
|
1743
|
-
ArrayOfstring (compound_id)
|
1744
|
-
|
1745
|
-
�㡧
|
1746
|
-
search_compounds_by_mass(174.05, 0.1)
|
1747
|
-
|
1748
|
-
--- search_drugs_by_mass(float:mass, float:range)
|
1749
|
-
|
1750
|
-
�ɥ�å���ʬ���̤Ǹ������ޤ���
|
1751
|
-
mass ���濴�Ȥ��� ��range �νŤ��Υɥ�å�����������ޤ���
|
1752
|
-
|
1753
|
-
���͡�
|
1754
|
-
ArrayOfstring (drug_id)
|
1755
|
-
|
1756
|
-
�㡧
|
1757
|
-
search_drugs_by_mass(150, 1.0)
|
1758
|
-
|
1759
|
-
--- search_glycans_by_mass(float:mass, float:range)
|
1760
|
-
|
1761
|
-
������ʬ���̤Ǹ������ޤ���
|
1762
|
-
mass ���濴�Ȥ��� ��range �νŤ�����������������ޤ���
|
1763
|
-
|
1764
|
-
���͡�
|
1765
|
-
ArrayOfstring
|
1766
|
-
|
1767
|
-
�㡧
|
1768
|
-
search_glycans_by_mass(1200, 0.5)
|
1769
|
-
|
1770
|
-
--- search_compounds_by_subcomp(string:mol, int:offset, int:limit)
|
1771
|
-
|
1772
|
-
������ʬ��¤����IJ���ʪ�� subcomp �ץ�������ȤäƸ������ޤ���
|
1773
|
-
|
1774
|
-
���饤����Ȥ��줿������ʬ�ΥΡ����ֹ椬������֤����Τǡ�
|
1775
|
-
���饤����Ȥ��줿����ʪ�ι�¤�� bget ���ޥ�ɤ� "-f m"
|
1776
|
-
���ץ�����Ĥ��� MOL �ե����ޥåȤǼ��������б����ǧ���ޤ���
|
1777
|
-
|
1778
|
-
���͡�
|
1779
|
-
ArrayOfStructureAlignment
|
1780
|
-
|
1781
|
-
�㡧
|
1782
|
-
mol = bget("-f m cpd:C00111")
|
1783
|
-
search_compounds_by_subcomp(mol, 1, 5)
|
1784
|
-
|
1785
|
-
��Ϣ URL��
|
1786
|
-
* ((<URL:http://www.genome.jp/ligand-bin/search_compound>))
|
1787
|
-
|
1788
|
-
--- search_drugs_by_subcomp(string:mol, int:offset, int:limit)
|
1789
|
-
|
1790
|
-
������ʬ��¤����ĥɥ�å��� subcomp �ץ�������ȤäƸ������ޤ���
|
1791
|
-
|
1792
|
-
���饤����Ȥ��줿������ʬ�ΥΡ����ֹ椬������֤����Τǡ�
|
1793
|
-
���饤����Ȥ��줿�ɥ�å��ι�¤�� bget ���ޥ�ɤ� "-f m"
|
1794
|
-
���ץ�����Ĥ��� MOL �ե����ޥåȤǼ��������б����ǧ���ޤ���
|
1795
|
-
|
1796
|
-
���͡�
|
1797
|
-
ArrayOfStructureAlignment
|
1798
|
-
|
1799
|
-
�㡧
|
1800
|
-
mol = bget("-f m dr:D00201")
|
1801
|
-
search_drugs_by_subcomp(mol, 1, 5)
|
1802
|
-
|
1803
|
-
��Ϣ URL��
|
1804
|
-
* ((<URL:http://www.genome.jp/ligand-bin/search_compound>))
|
1805
|
-
|
1806
|
-
--- search_glycans_by_kcam(string:kcf, string:program, string:option, int:offset, int:limit)
|
1807
|
-
|
1808
|
-
������ʬ��¤����������� KCaM �ץ�������ȤäƸ������ޤ���
|
1809
|
-
|
1810
|
-
������ program �ˤ� approximate �ޥå���Ԥ� "gapped" �ޤ���
|
1811
|
-
exact �ޥå���Ԥ� "ungapped" ����ꤷ�ޤ����ޤ� option �ˤ�
|
1812
|
-
"global" �ޤ��� "local" ����ꤷ�ޤ���
|
1813
|
-
|
1814
|
-
���饤����Ȥ��줿������ʬ�ΥΡ����ֹ椬������֤����Τǡ�
|
1815
|
-
���饤����Ȥ��줿�����ι�¤�� bget ���ޥ�ɤ� "-f k"
|
1816
|
-
���ץ�����Ĥ��� KCF �ե����ޥåȤǼ��������б����ǧ���ޤ���
|
1817
|
-
|
1818
|
-
���͡�
|
1819
|
-
ArrayOfStructureAlignment
|
1820
|
-
|
1821
|
-
�㡧
|
1822
|
-
kcf = bget("-f k gl:G12922")
|
1823
|
-
search_glycans_by_kcam(kcf, "gapped", "local", 1, 5)
|
1824
|
-
|
1825
|
-
��Ϣ URL��
|
1826
|
-
* ((<URL:http://www.genome.jp/ligand-bin/search_glycan.cgi>))
|
1827
|
-
* ((<URL:http://www.genome.jp/ligand/kcam/>))
|
1828
|
-
|
1829
|
-
== Notes
|
1830
|
-
|
1831
|
-
Last updated: December 27, 2006
|
1832
|
-
|
1833
|
-
=end
|
1834
|
-
|