jandot-bio 1.2.1
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- data/bin/bioruby +44 -0
- data/bin/br_biofetch.rb +47 -0
- data/bin/br_bioflat.rb +282 -0
- data/bin/br_biogetseq.rb +45 -0
- data/bin/br_pmfetch.rb +421 -0
- data/doc/Changes-0.7.rd +369 -0
- data/doc/KEGG_API.rd +1843 -0
- data/doc/KEGG_API.rd.ja +1834 -0
- data/doc/Tutorial.rd +1296 -0
- data/doc/Tutorial.rd.ja +2640 -0
- data/etc/bioinformatics/seqdatabase.ini +210 -0
- data/lib/bio.rb +279 -0
- data/lib/bio/alignment.rb +2518 -0
- data/lib/bio/appl/bl2seq/report.rb +334 -0
- data/lib/bio/appl/blast.rb +351 -0
- data/lib/bio/appl/blast/format0.rb +1438 -0
- data/lib/bio/appl/blast/format8.rb +83 -0
- data/lib/bio/appl/blast/report.rb +516 -0
- data/lib/bio/appl/blast/rexml.rb +135 -0
- data/lib/bio/appl/blast/rpsblast.rb +176 -0
- data/lib/bio/appl/blast/wublast.rb +550 -0
- data/lib/bio/appl/blast/xmlparser.rb +228 -0
- data/lib/bio/appl/blat/report.rb +489 -0
- data/lib/bio/appl/clustalw.rb +219 -0
- data/lib/bio/appl/clustalw/report.rb +152 -0
- data/lib/bio/appl/emboss.rb +203 -0
- data/lib/bio/appl/fasta.rb +237 -0
- data/lib/bio/appl/fasta/format10.rb +325 -0
- data/lib/bio/appl/gcg/msf.rb +212 -0
- data/lib/bio/appl/gcg/seq.rb +195 -0
- data/lib/bio/appl/genscan/report.rb +552 -0
- data/lib/bio/appl/hmmer.rb +126 -0
- data/lib/bio/appl/hmmer/report.rb +683 -0
- data/lib/bio/appl/iprscan/report.rb +374 -0
- data/lib/bio/appl/mafft.rb +259 -0
- data/lib/bio/appl/mafft/report.rb +226 -0
- data/lib/bio/appl/muscle.rb +52 -0
- data/lib/bio/appl/phylip/alignment.rb +129 -0
- data/lib/bio/appl/phylip/distance_matrix.rb +96 -0
- data/lib/bio/appl/probcons.rb +41 -0
- data/lib/bio/appl/psort.rb +548 -0
- data/lib/bio/appl/psort/report.rb +457 -0
- data/lib/bio/appl/pts1.rb +263 -0
- data/lib/bio/appl/sim4.rb +124 -0
- data/lib/bio/appl/sim4/report.rb +485 -0
- data/lib/bio/appl/sosui/report.rb +151 -0
- data/lib/bio/appl/spidey/report.rb +593 -0
- data/lib/bio/appl/targetp/report.rb +267 -0
- data/lib/bio/appl/tcoffee.rb +55 -0
- data/lib/bio/appl/tmhmm/report.rb +222 -0
- data/lib/bio/command.rb +337 -0
- data/lib/bio/data/aa.rb +349 -0
- data/lib/bio/data/codontable.rb +722 -0
- data/lib/bio/data/na.rb +223 -0
- data/lib/bio/db.rb +329 -0
- data/lib/bio/db/aaindex.rb +357 -0
- data/lib/bio/db/embl/common.rb +336 -0
- data/lib/bio/db/embl/embl.rb +402 -0
- data/lib/bio/db/embl/sptr.rb +1283 -0
- data/lib/bio/db/embl/swissprot.rb +42 -0
- data/lib/bio/db/embl/trembl.rb +41 -0
- data/lib/bio/db/embl/uniprot.rb +42 -0
- data/lib/bio/db/fantom.rb +599 -0
- data/lib/bio/db/fasta.rb +907 -0
- data/lib/bio/db/genbank/common.rb +290 -0
- data/lib/bio/db/genbank/ddbj.rb +22 -0
- data/lib/bio/db/genbank/genbank.rb +215 -0
- data/lib/bio/db/genbank/genpept.rb +60 -0
- data/lib/bio/db/genbank/refseq.rb +18 -0
- data/lib/bio/db/gff.rb +174 -0
- data/lib/bio/db/go.rb +481 -0
- data/lib/bio/db/kegg/brite.rb +41 -0
- data/lib/bio/db/kegg/compound.rb +131 -0
- data/lib/bio/db/kegg/drug.rb +98 -0
- data/lib/bio/db/kegg/enzyme.rb +148 -0
- data/lib/bio/db/kegg/expression.rb +155 -0
- data/lib/bio/db/kegg/genes.rb +263 -0
- data/lib/bio/db/kegg/genome.rb +241 -0
- data/lib/bio/db/kegg/glycan.rb +170 -0
- data/lib/bio/db/kegg/keggtab.rb +357 -0
- data/lib/bio/db/kegg/kgml.rb +256 -0
- data/lib/bio/db/kegg/orthology.rb +136 -0
- data/lib/bio/db/kegg/reaction.rb +82 -0
- data/lib/bio/db/kegg/taxonomy.rb +331 -0
- data/lib/bio/db/lasergene.rb +209 -0
- data/lib/bio/db/litdb.rb +107 -0
- data/lib/bio/db/medline.rb +323 -0
- data/lib/bio/db/nbrf.rb +191 -0
- data/lib/bio/db/newick.rb +658 -0
- data/lib/bio/db/nexus.rb +1854 -0
- data/lib/bio/db/pdb.rb +29 -0
- data/lib/bio/db/pdb/atom.rb +77 -0
- data/lib/bio/db/pdb/chain.rb +210 -0
- data/lib/bio/db/pdb/chemicalcomponent.rb +224 -0
- data/lib/bio/db/pdb/model.rb +148 -0
- data/lib/bio/db/pdb/pdb.rb +1911 -0
- data/lib/bio/db/pdb/residue.rb +176 -0
- data/lib/bio/db/pdb/utils.rb +399 -0
- data/lib/bio/db/prosite.rb +597 -0
- data/lib/bio/db/rebase.rb +457 -0
- data/lib/bio/db/soft.rb +404 -0
- data/lib/bio/db/transfac.rb +375 -0
- data/lib/bio/feature.rb +226 -0
- data/lib/bio/io/das.rb +461 -0
- data/lib/bio/io/dbget.rb +194 -0
- data/lib/bio/io/ddbjxml.rb +581 -0
- data/lib/bio/io/ebisoap.rb +158 -0
- data/lib/bio/io/ensembl.rb +229 -0
- data/lib/bio/io/fastacmd.rb +163 -0
- data/lib/bio/io/fetch.rb +181 -0
- data/lib/bio/io/flatfile.rb +1309 -0
- data/lib/bio/io/flatfile/bdb.rb +253 -0
- data/lib/bio/io/flatfile/index.rb +1371 -0
- data/lib/bio/io/flatfile/indexer.rb +787 -0
- data/lib/bio/io/higet.rb +73 -0
- data/lib/bio/io/hinv.rb +442 -0
- data/lib/bio/io/keggapi.rb +805 -0
- data/lib/bio/io/ncbirest.rb +256 -0
- data/lib/bio/io/ncbisoap.rb +155 -0
- data/lib/bio/io/pubmed.rb +307 -0
- data/lib/bio/io/registry.rb +292 -0
- data/lib/bio/io/soapwsdl.rb +119 -0
- data/lib/bio/io/sql.rb +365 -0
- data/lib/bio/location.rb +772 -0
- data/lib/bio/map.rb +410 -0
- data/lib/bio/pathway.rb +854 -0
- data/lib/bio/reference.rb +623 -0
- data/lib/bio/sequence.rb +475 -0
- data/lib/bio/sequence/aa.rb +125 -0
- data/lib/bio/sequence/common.rb +333 -0
- data/lib/bio/sequence/compat.rb +123 -0
- data/lib/bio/sequence/format.rb +181 -0
- data/lib/bio/sequence/generic.rb +24 -0
- data/lib/bio/sequence/na.rb +491 -0
- data/lib/bio/shell.rb +44 -0
- data/lib/bio/shell/core.rb +578 -0
- data/lib/bio/shell/demo.rb +146 -0
- data/lib/bio/shell/interface.rb +218 -0
- data/lib/bio/shell/irb.rb +95 -0
- data/lib/bio/shell/object.rb +71 -0
- data/lib/bio/shell/plugin/blast.rb +42 -0
- data/lib/bio/shell/plugin/codon.rb +218 -0
- data/lib/bio/shell/plugin/das.rb +58 -0
- data/lib/bio/shell/plugin/emboss.rb +23 -0
- data/lib/bio/shell/plugin/entry.rb +105 -0
- data/lib/bio/shell/plugin/flatfile.rb +101 -0
- data/lib/bio/shell/plugin/keggapi.rb +181 -0
- data/lib/bio/shell/plugin/midi.rb +430 -0
- data/lib/bio/shell/plugin/obda.rb +45 -0
- data/lib/bio/shell/plugin/psort.rb +56 -0
- data/lib/bio/shell/plugin/seq.rb +247 -0
- data/lib/bio/shell/plugin/soap.rb +87 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb +29 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml +27 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml +11 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml +7 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +368 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml +47 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb +144 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb +47 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +8 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml +10 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml +26 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif +0 -0
- data/lib/bio/shell/script.rb +25 -0
- data/lib/bio/shell/setup.rb +109 -0
- data/lib/bio/shell/web.rb +102 -0
- data/lib/bio/tree.rb +850 -0
- data/lib/bio/util/color_scheme.rb +191 -0
- data/lib/bio/util/color_scheme/buried.rb +59 -0
- data/lib/bio/util/color_scheme/helix.rb +59 -0
- data/lib/bio/util/color_scheme/hydropathy.rb +64 -0
- data/lib/bio/util/color_scheme/nucleotide.rb +31 -0
- data/lib/bio/util/color_scheme/strand.rb +59 -0
- data/lib/bio/util/color_scheme/taylor.rb +50 -0
- data/lib/bio/util/color_scheme/turn.rb +59 -0
- data/lib/bio/util/color_scheme/zappo.rb +50 -0
- data/lib/bio/util/contingency_table.rb +370 -0
- data/lib/bio/util/restriction_enzyme.rb +228 -0
- data/lib/bio/util/restriction_enzyme/analysis.rb +249 -0
- data/lib/bio/util/restriction_enzyme/analysis_basic.rb +217 -0
- data/lib/bio/util/restriction_enzyme/cut_symbol.rb +107 -0
- data/lib/bio/util/restriction_enzyme/double_stranded.rb +321 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb +130 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb +103 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb +38 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb +76 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb +107 -0
- data/lib/bio/util/restriction_enzyme/enzymes.yaml +7061 -0
- data/lib/bio/util/restriction_enzyme/range/cut_range.rb +24 -0
- data/lib/bio/util/restriction_enzyme/range/cut_ranges.rb +47 -0
- data/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb +67 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +257 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +242 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +51 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb +41 -0
- data/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb +77 -0
- data/lib/bio/util/restriction_enzyme/single_strand.rb +199 -0
- data/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb +135 -0
- data/lib/bio/util/restriction_enzyme/single_strand_complement.rb +23 -0
- data/lib/bio/util/restriction_enzyme/string_formatting.rb +111 -0
- data/lib/bio/util/sirna.rb +288 -0
- data/sample/any2fasta.rb +59 -0
- data/sample/biofetch.rb +475 -0
- data/sample/color_scheme_na.rb +91 -0
- data/sample/dbget +37 -0
- data/sample/enzymes.rb +78 -0
- data/sample/fasta2tab.rb +99 -0
- data/sample/fastagrep.rb +72 -0
- data/sample/fastasort.rb +54 -0
- data/sample/fsplit.rb +51 -0
- data/sample/gb2fasta.rb +30 -0
- data/sample/gb2tab.rb +325 -0
- data/sample/gbtab2mysql.rb +161 -0
- data/sample/genes2nuc.rb +33 -0
- data/sample/genes2pep.rb +33 -0
- data/sample/genes2tab.rb +81 -0
- data/sample/genome2rb.rb +29 -0
- data/sample/genome2tab.rb +76 -0
- data/sample/goslim.rb +303 -0
- data/sample/gt2fasta.rb +47 -0
- data/sample/na2aa.rb +34 -0
- data/sample/pmfetch.rb +42 -0
- data/sample/pmsearch.rb +42 -0
- data/sample/psortplot_html.rb +214 -0
- data/sample/ssearch2tab.rb +96 -0
- data/sample/tdiary.rb +158 -0
- data/sample/tfastx2tab.rb +100 -0
- data/sample/vs-genes.rb +212 -0
- data/test/data/HMMER/hmmpfam.out +64 -0
- data/test/data/HMMER/hmmsearch.out +88 -0
- data/test/data/SOSUI/sample.report +11 -0
- data/test/data/TMHMM/sample.report +21 -0
- data/test/data/aaindex/DAYM780301 +30 -0
- data/test/data/aaindex/PRAM900102 +20 -0
- data/test/data/bl2seq/cd8a_cd8b_blastp.bl2seq +53 -0
- data/test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq +37 -0
- data/test/data/blast/2.2.15.blastp.m7 +876 -0
- data/test/data/blast/b0002.faa +15 -0
- data/test/data/blast/b0002.faa.m0 +128 -0
- data/test/data/blast/b0002.faa.m7 +65 -0
- data/test/data/blast/b0002.faa.m8 +1 -0
- data/test/data/embl/AB090716.embl +65 -0
- data/test/data/embl/AB090716.embl.rel89 +63 -0
- data/test/data/fasta/example1.txt +75 -0
- data/test/data/fasta/example2.txt +21 -0
- data/test/data/genscan/sample.report +63 -0
- data/test/data/iprscan/merged.raw +32 -0
- data/test/data/iprscan/merged.txt +74 -0
- data/test/data/prosite/prosite.dat +2233 -0
- data/test/data/refseq/nm_126355.entret +64 -0
- data/test/data/soft/GDS100_partial.soft +92 -0
- data/test/data/soft/GSE3457_family_partial.soft +874 -0
- data/test/data/uniprot/p53_human.uniprot +1456 -0
- data/test/functional/bio/io/test_ensembl.rb +186 -0
- data/test/functional/bio/io/test_soapwsdl.rb +52 -0
- data/test/runner.rb +14 -0
- data/test/unit/bio/appl/bl2seq/test_report.rb +134 -0
- data/test/unit/bio/appl/blast/test_report.rb +417 -0
- data/test/unit/bio/appl/blast/test_xmlparser.rb +388 -0
- data/test/unit/bio/appl/genscan/test_report.rb +182 -0
- data/test/unit/bio/appl/hmmer/test_report.rb +342 -0
- data/test/unit/bio/appl/iprscan/test_report.rb +338 -0
- data/test/unit/bio/appl/mafft/test_report.rb +63 -0
- data/test/unit/bio/appl/sosui/test_report.rb +81 -0
- data/test/unit/bio/appl/targetp/test_report.rb +146 -0
- data/test/unit/bio/appl/test_blast.rb +163 -0
- data/test/unit/bio/appl/test_fasta.rb +130 -0
- data/test/unit/bio/appl/test_pts1.rb +140 -0
- data/test/unit/bio/appl/tmhmm/test_report.rb +126 -0
- data/test/unit/bio/data/test_aa.rb +90 -0
- data/test/unit/bio/data/test_codontable.rb +107 -0
- data/test/unit/bio/data/test_na.rb +80 -0
- data/test/unit/bio/db/embl/test_common.rb +117 -0
- data/test/unit/bio/db/embl/test_embl.rb +214 -0
- data/test/unit/bio/db/embl/test_embl_rel89.rb +219 -0
- data/test/unit/bio/db/embl/test_sptr.rb +1775 -0
- data/test/unit/bio/db/embl/test_uniprot.rb +31 -0
- data/test/unit/bio/db/kegg/test_genes.rb +45 -0
- data/test/unit/bio/db/pdb/test_pdb.rb +152 -0
- data/test/unit/bio/db/test_aaindex.rb +197 -0
- data/test/unit/bio/db/test_fasta.rb +250 -0
- data/test/unit/bio/db/test_gff.rb +127 -0
- data/test/unit/bio/db/test_lasergene.rb +95 -0
- data/test/unit/bio/db/test_newick.rb +293 -0
- data/test/unit/bio/db/test_nexus.rb +360 -0
- data/test/unit/bio/db/test_prosite.rb +1437 -0
- data/test/unit/bio/db/test_rebase.rb +101 -0
- data/test/unit/bio/db/test_soft.rb +138 -0
- data/test/unit/bio/io/test_ddbjxml.rb +75 -0
- data/test/unit/bio/io/test_ensembl.rb +109 -0
- data/test/unit/bio/io/test_fastacmd.rb +42 -0
- data/test/unit/bio/io/test_flatfile.rb +237 -0
- data/test/unit/bio/io/test_soapwsdl.rb +32 -0
- data/test/unit/bio/sequence/test_aa.rb +103 -0
- data/test/unit/bio/sequence/test_common.rb +174 -0
- data/test/unit/bio/sequence/test_compat.rb +69 -0
- data/test/unit/bio/sequence/test_na.rb +330 -0
- data/test/unit/bio/shell/plugin/test_seq.rb +185 -0
- data/test/unit/bio/test_alignment.rb +1025 -0
- data/test/unit/bio/test_command.rb +288 -0
- data/test/unit/bio/test_db.rb +96 -0
- data/test/unit/bio/test_feature.rb +116 -0
- data/test/unit/bio/test_location.rb +39 -0
- data/test/unit/bio/test_map.rb +230 -0
- data/test/unit/bio/test_pathway.rb +473 -0
- data/test/unit/bio/test_reference.rb +224 -0
- data/test/unit/bio/test_sequence.rb +329 -0
- data/test/unit/bio/test_shell.rb +18 -0
- data/test/unit/bio/test_tree.rb +593 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb +299 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb +103 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb +240 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb +101 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb +75 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb +73 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb +53 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb +104 -0
- data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb +83 -0
- data/test/unit/bio/util/restriction_enzyme/test_analysis.rb +246 -0
- data/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb +44 -0
- data/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb +115 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb +60 -0
- data/test/unit/bio/util/test_color_scheme.rb +33 -0
- data/test/unit/bio/util/test_contingency_table.rb +94 -0
- data/test/unit/bio/util/test_restriction_enzyme.rb +42 -0
- data/test/unit/bio/util/test_sirna.rb +245 -0
- metadata +479 -0
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���
|
15
|
+
|
16
|
+
== �ܼ�
|
17
|
+
|
18
|
+
* ((<����ȥ����������>))
|
19
|
+
* ((<KEGG API �λȤ���>))
|
20
|
+
* ((<Ruby ��>))
|
21
|
+
* ((<Perl ��>))
|
22
|
+
* ((<Perl ��������>))
|
23
|
+
* ((<Python ��>))
|
24
|
+
* ((<Java ��>))
|
25
|
+
* ((<KEGG API ��ե����>))
|
26
|
+
* ((<WSDL �ե�����>))
|
27
|
+
* ((<�Ѹ������>))
|
28
|
+
* ((<����ͤΥǡ�����>))
|
29
|
+
* ((<SSDBRelation ��>)), ((<ArrayOfSSDBRelation ��>))
|
30
|
+
* ((<MotifResult ��>)), ((<ArrayOfMotifResult ��>))
|
31
|
+
* ((<Definition ��>)), ((<ArrayOfDefinition ��>))
|
32
|
+
* ((<LinkDBRelation ��>)), ((<ArrayOfLinkDBRelation ��>))
|
33
|
+
* ((<PathwayElement ��>)), ((<ArrayOfPathwayElement ��>))
|
34
|
+
* ((<PathwayElementRelation ��>)), ((<ArrayOfPathwayElementRelation ��>))
|
35
|
+
* ((<Subtype ��>)), ((<ArrayOfSubtype ��>))
|
36
|
+
* ((<StructureAlignment ��>)), ((<ArrayOfStructureAlignment ��>))
|
37
|
+
* ((<��åɰ���>))
|
38
|
+
* ((<�����>))
|
39
|
+
* ((<list_databases>))
|
40
|
+
* ((<list_organisms>))
|
41
|
+
* ((<list_pathways>))
|
42
|
+
* ((<DBGET>))
|
43
|
+
* ((<binfo>))
|
44
|
+
* ((<bfind>))
|
45
|
+
* ((<bget>))
|
46
|
+
* ((<btit>))
|
47
|
+
* ((<bconv>))
|
48
|
+
* ((<LinkDB>))
|
49
|
+
* ((<�ǡ����١����֤Υ��>))
|
50
|
+
* ((<get_linkdb_by_entry>))
|
51
|
+
* ((<get_linkdb_between_databases>))
|
52
|
+
* ((<�����Ҥȹ����ֹ�δط�>))
|
53
|
+
* ((<get_genes_by_enzyme>))
|
54
|
+
* ((<get_enzymes_by_gene>))
|
55
|
+
* ((<���ǡ�����ʪ���ꥢ�������δط�>))
|
56
|
+
* ((<get_enzymes_by_compound>))
|
57
|
+
* ((<get_enzymes_by_glycan>))
|
58
|
+
* ((<get_enzymes_by_reaction>))
|
59
|
+
* ((<get_compounds_by_enzyme>))
|
60
|
+
* ((<get_compounds_by_reaction>))
|
61
|
+
* ((<get_glycans_by_enzyme>))
|
62
|
+
* ((<get_glycans_by_reaction>))
|
63
|
+
* ((<get_reactions_by_enzyme>))
|
64
|
+
* ((<get_reactions_by_compound>))
|
65
|
+
* ((<get_reactions_by_glycan>))
|
66
|
+
* ((<SSDB>))
|
67
|
+
* ((<get_best_best_neighbors_by_gene>))
|
68
|
+
* ((<get_best_neighbors_by_gene>))
|
69
|
+
* ((<get_reverse_best_neighbors_by_gene>))
|
70
|
+
* ((<get_paralogs_by_gene>))
|
71
|
+
* ((<Motif>))
|
72
|
+
* ((<get_motifs_by_gene>))
|
73
|
+
* ((<get_genes_by_motifs>))
|
74
|
+
* ((<KO>))
|
75
|
+
* ((<get_ko_by_gene>))
|
76
|
+
* ((<get_ko_by_ko_class>))
|
77
|
+
* ((<get_genes_by_ko_class>))
|
78
|
+
* ((<get_genes_by_ko>))
|
79
|
+
* ((<PATHWAY>))
|
80
|
+
* ((<�ѥ��������ؤο��Ť�>))
|
81
|
+
* ((<mark_pathway_by_objects>))
|
82
|
+
* ((<color_pathway_by_objects>))
|
83
|
+
* ((<color_pathway_by_elements>))
|
84
|
+
* ((<get_html_of_marked_pathway_by_objects>))
|
85
|
+
* ((<get_html_of_colored_pathway_by_objects>))
|
86
|
+
* ((<get_html_of_colored_pathway_by_elements>))
|
87
|
+
* ((<�ѥ���������Υ��֥������ȴ֤δط�>))
|
88
|
+
* ((<get_element_relations_by_pathway>))
|
89
|
+
* ((<�ѥ���������Υ��֥������ȸ���>))
|
90
|
+
* ((<get_elements_by_pathway>))
|
91
|
+
* ((<get_genes_by_pathway>))
|
92
|
+
* ((<get_enzymes_by_pathway>))
|
93
|
+
* ((<get_compounds_by_pathway>))
|
94
|
+
* ((<get_glycans_by_pathway>))
|
95
|
+
* ((<get_reactions_by_pathway>))
|
96
|
+
* ((<get_kos_by_pathway>))
|
97
|
+
* ((<���֥������Ȥ���ѥ�����������>))
|
98
|
+
* ((<get_pathways_by_genes>))
|
99
|
+
* ((<get_pathways_by_enzymes>))
|
100
|
+
* ((<get_pathways_by_compounds>))
|
101
|
+
* ((<get_pathways_by_glycans>))
|
102
|
+
* ((<get_pathways_by_reactions>))
|
103
|
+
* ((<get_pathways_by_kos>))
|
104
|
+
* ((<�ѥ��������֤δط�>))
|
105
|
+
* ((<get_linked_pathways>))
|
106
|
+
* ((<GENES>))
|
107
|
+
* ((<get_genes_by_organism>))
|
108
|
+
* ((<GENOME>))
|
109
|
+
* ((<get_number_of_genes_by_organism>))
|
110
|
+
* ((<LIGAND>))
|
111
|
+
* ((<convert_mol_to_kcf>))
|
112
|
+
* ((<search_compounds_by_name>))
|
113
|
+
* ((<search_drugs_by_name>))
|
114
|
+
* ((<search_glycans_by_name>))
|
115
|
+
* ((<search_compounds_by_composition>))
|
116
|
+
* ((<search_drugs_by_composition>))
|
117
|
+
* ((<search_glycans_by_composition>))
|
118
|
+
* ((<search_compounds_by_mass>))
|
119
|
+
* ((<search_drugs_by_mass>))
|
120
|
+
* ((<search_glycans_by_mass>))
|
121
|
+
* ((<search_compounds_by_subcomp>))
|
122
|
+
* ((<search_drugs_by_subcomp>))
|
123
|
+
* ((<search_glycans_by_kcam>))
|
124
|
+
|
125
|
+
== ����ȥ����������
|
126
|
+
|
127
|
+
�����֥����ӥ��Ȥϡ����饤����Ȥ��������ͥåȤ�𤷤ƥ����Ф�
|
128
|
+
���ꡢ�����Ф��ץ������μ¹Է�̤饤����Ȥ��֤����Ȥߤǡ�����Ū�ˤ�
|
129
|
+
�����֥ڡ����ǻȤ��� HTTP �ץ��ȥ���ȡ���¤����ĥǡ�����ɽ����ˡ�Ȥ���
|
130
|
+
��ڤ��Ƥ��� XML �ޡ������å�ʸ��������Ѥ�����Τ�ؤ��ޤ���
|
131
|
+
|
132
|
+
�����֥����ӥ��ϥץ�����फ�����ѤǤ��뤿�ᡢ���Ū�˸�����Ԥä��ꡢ
|
133
|
+
���������ͤ��Ѥ����͡������ưŪ�˽��������ꤹ��Τ˸����Ƥ��ޤ���
|
134
|
+
���Τ��ᡢ������ŷ��������䤤��碌��Google �ؤ�ʣ�縡���ʤɤǤ�Ȥ���
|
135
|
+
���ޤ���
|
136
|
+
|
137
|
+
HTTP ���Ѥ�����åȤˤϡ�ï�Ǥ�Ȥ��뤳�Ȥ�ե�������������ʤɤ����¤�
|
138
|
+
�����ˤ������Ȥ����ꡢXML �����ˤϴ�Ϣ���Ѥ�·�äƤ��뤳�Ȥ�ʣ���ʥǡ���
|
139
|
+
��¤��ɽ���Ǥ���Ȥ��ä��ݥ���Ȥ�����ޤ���
|
140
|
+
|
141
|
+
�����֥����ӥ��Ǥ� XML ��Ϣ���Ѥ���Ǥ� SOAP �� WSDL ��Ȥ����Ȥ�¿���ʤä�
|
142
|
+
���ޤ���SOAP �ϥ��饤����Ȥȥ����Ф����Ȥꤹ���å�������ɽ����ˡ��
|
143
|
+
ɸ�ಽ������Τǡ������� Simple Object Access Method ��ά�Ȥ���Ƥ��ޤ���
|
144
|
+
(���� Service Oriented Access Protocol �Ȥ������Ȥ⤢��褦�Ǥ�)��
|
145
|
+
WSDL �� SOAP �˴�Ť������ӥ���ԥ塼������ñ�����ѤǤ���褦�ˤ���
|
146
|
+
����Τ�Τǡ�Web Service Description Language ��ά�ȤʤäƤ��ޤ���
|
147
|
+
|
148
|
+
KEGG API �Ϥ����ε��Ѥ�Ȥäơ���ʬ�ζ�̣��������Ҥ�ѥ��������ʤɤ�
|
149
|
+
�����ͳ�˸�����������Ϥ��Ѥ����ꤹ�뤿��μ��ʤ����ޤ����桼����
|
150
|
+
KEGG ��¿���ε�ǽ�����֥ڡ�����å���������˼�ʬ�Υץ�������
|
151
|
+
�椫�鼡���ȼ¹Ԥ��뤳�Ȥ��Ǥ���褦�ˤʤ�ޤ���
|
152
|
+
|
153
|
+
KEGG API �˴ؤ���ǿ��ξ���ϰʲ��� URL �������뤳�Ȥ��Ǥ��ޤ���
|
154
|
+
|
155
|
+
* ((<URL:http://www.genome.jp/kegg/soap/>))
|
156
|
+
|
157
|
+
== KEGG API �λȤ���
|
158
|
+
|
159
|
+
�ʲ��Ǥ� Ruby, Perl, Python, Java �γƸ���ˤ�� KEGG API �δ�ñ�ʻȤ�����
|
160
|
+
�Ҳ𤷤ޤ����Ƹ���� SOAP �� WSDL ����饤�֥����ɲå��ȡ��뤹��
|
161
|
+
ɬ�פ�����ޤ���
|
162
|
+
|
163
|
+
=== Ruby ��
|
164
|
+
|
165
|
+
Ruby 1.8.1 �ʹߤǤϡ�ɸ��� SOAP ��Ȥ������Ǥ��ޤ��Τ��ɲå��ȡ�
|
166
|
+
���ɬ�פ���ޤ���
|
167
|
+
|
168
|
+
Ruby 1.8.0 �Ǥ�
|
169
|
+
((<SOAP4R|URL:http://raa.ruby-lang.org/list.rhtml?name=soap4r>)),
|
170
|
+
((<devel-logger|URL:http://raa.ruby-lang.org/list.rhtml?name=devel-logger>)),
|
171
|
+
((<http-access2|URL:http://raa.ruby-lang.org/list.rhtml?name=http-access2>))
|
172
|
+
�ʤɤΥ饤�֥��ȡ��뤹��ɬ�פ�����ޤ���
|
173
|
+
|
174
|
+
Ruby 1.6.8 �ξ��Ϥ���� SOAP4R ��ɬ�פȤ���¾�Υ饤�֥�� (date2, uconv,
|
175
|
+
XML �Υѡ����ʤ�) �⥤�ȡ��뤹��ɬ�פ�����ޤ��Τǡ����餫���� SOAP4R
|
176
|
+
�Υɥ�����Ȥ˽��ä�����Ƥ����ޤ���
|
177
|
+
|
178
|
+
�ʲ��Υ���ץ륳���ɤϡ���IJ�ݤ� b0002 �����ҤȺǤ���Ʊ���ι⤤������
|
179
|
+
��Smith-Waterman �������ι⤤��� 5 �ĸ�������ɽ������ץ������Ǥ���
|
180
|
+
|
181
|
+
#!/usr/bin/env ruby
|
182
|
+
|
183
|
+
require 'soap/wsdlDriver'
|
184
|
+
|
185
|
+
wsdl = "http://soap.genome.jp/KEGG.wsdl"
|
186
|
+
serv = SOAP::WSDLDriverFactory.new(wsdl).create_rpc_driver
|
187
|
+
serv.generate_explicit_type = true # SOAP �� Ruby �η��Ѵ���ͭ���ˤ���
|
188
|
+
|
189
|
+
offset = 1
|
190
|
+
limit = 5
|
191
|
+
|
192
|
+
top5 = serv.get_best_neighbors_by_gene('eco:b0002', offset, limit)
|
193
|
+
top5.each do |hit|
|
194
|
+
print hit.genes_id1, "\t", hit.genes_id2, "\t", hit.sw_score, "\n"
|
195
|
+
end
|
196
|
+
|
197
|
+
�ץ���������� 'get_best_neighbors_by_gene' �ϡ�KEGG �� SSDB �ǡ���
|
198
|
+
�١�����Ȥä� KEGG �� GENES �˴ޤޤ�Ƥ������ʪ����椫��Ǥ���Ʊ��
|
199
|
+
�ι⤤�����Ҥ�õ���Ƥ��� API �Ǥ�����̤ϼ��Τ褦��ɽ������ޤ���
|
200
|
+
|
201
|
+
eco:b0002 eco:b0002 5283
|
202
|
+
eco:b0002 ecj:JW0001 5283
|
203
|
+
eco:b0002 sfx:S0002 5271
|
204
|
+
eco:b0002 sfl:SF0002 5271
|
205
|
+
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
|
+
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
|
+
���̤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
|
+
|