bio 1.0.0 → 1.1.0
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- data/bin/bioruby +14 -122
- data/bin/br_biofetch.rb +2 -2
- data/bin/br_bioflat.rb +2 -2
- data/bin/br_biogetseq.rb +2 -2
- data/bin/br_pmfetch.rb +3 -3
- data/doc/Changes-0.7.rd +77 -0
- data/doc/KEGG_API.rd +523 -232
- data/doc/KEGG_API.rd.ja +529 -207
- data/doc/Tutorial.rd +48 -11
- data/lib/bio.rb +59 -6
- data/lib/bio/alignment.rb +713 -103
- data/lib/bio/appl/bl2seq/report.rb +2 -18
- data/lib/bio/appl/blast.rb +108 -91
- data/lib/bio/appl/blast/format0.rb +33 -18
- data/lib/bio/appl/blast/format8.rb +6 -20
- data/lib/bio/appl/blast/report.rb +293 -429
- data/lib/bio/appl/blast/rexml.rb +8 -22
- data/lib/bio/appl/blast/wublast.rb +21 -12
- data/lib/bio/appl/blast/xmlparser.rb +180 -183
- data/lib/bio/appl/blat/report.rb +127 -30
- data/lib/bio/appl/clustalw.rb +87 -59
- data/lib/bio/appl/clustalw/report.rb +20 -22
- data/lib/bio/appl/emboss.rb +113 -20
- data/lib/bio/appl/fasta.rb +173 -198
- data/lib/bio/appl/fasta/format10.rb +244 -347
- 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 +5 -23
- data/lib/bio/appl/hmmer.rb +8 -45
- data/lib/bio/appl/hmmer/report.rb +2 -20
- data/lib/bio/appl/iprscan/report.rb +374 -0
- data/lib/bio/appl/mafft.rb +87 -50
- data/lib/bio/appl/mafft/report.rb +151 -44
- 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 +89 -96
- data/lib/bio/appl/psort/report.rb +6 -22
- data/lib/bio/appl/pts1.rb +263 -0
- data/lib/bio/appl/sim4.rb +26 -36
- data/lib/bio/appl/sim4/report.rb +2 -18
- data/lib/bio/appl/sosui/report.rb +5 -20
- data/lib/bio/appl/spidey/report.rb +2 -2
- data/lib/bio/appl/targetp/report.rb +4 -20
- data/lib/bio/appl/tcoffee.rb +55 -0
- data/lib/bio/appl/tmhmm/report.rb +4 -20
- data/lib/bio/command.rb +235 -64
- data/lib/bio/data/aa.rb +21 -26
- data/lib/bio/data/codontable.rb +2 -20
- data/lib/bio/data/na.rb +19 -4
- data/lib/bio/db.rb +27 -12
- data/lib/bio/db/aaindex.rb +2 -20
- data/lib/bio/db/embl/common.rb +4 -21
- data/lib/bio/db/embl/embl.rb +33 -85
- data/lib/bio/db/embl/sptr.rb +612 -302
- data/lib/bio/db/embl/swissprot.rb +10 -29
- data/lib/bio/db/embl/trembl.rb +10 -29
- data/lib/bio/db/embl/uniprot.rb +10 -29
- data/lib/bio/db/fantom.rb +15 -20
- data/lib/bio/db/fasta.rb +3 -3
- data/lib/bio/db/genbank/common.rb +37 -46
- data/lib/bio/db/genbank/ddbj.rb +6 -18
- data/lib/bio/db/genbank/genbank.rb +47 -186
- data/lib/bio/db/genbank/genpept.rb +4 -17
- data/lib/bio/db/genbank/refseq.rb +4 -17
- data/lib/bio/db/gff.rb +103 -35
- data/lib/bio/db/go.rb +4 -20
- data/lib/bio/db/kegg/brite.rb +26 -36
- data/lib/bio/db/kegg/compound.rb +81 -85
- data/lib/bio/db/kegg/drug.rb +98 -0
- data/lib/bio/db/kegg/enzyme.rb +133 -110
- data/lib/bio/db/kegg/expression.rb +2 -20
- data/lib/bio/db/kegg/genes.rb +208 -238
- data/lib/bio/db/kegg/genome.rb +164 -285
- data/lib/bio/db/kegg/glycan.rb +114 -157
- data/lib/bio/db/kegg/keggtab.rb +242 -303
- data/lib/bio/db/kegg/kgml.rb +117 -160
- data/lib/bio/db/kegg/orthology.rb +112 -0
- data/lib/bio/db/kegg/reaction.rb +54 -69
- data/lib/bio/db/kegg/taxonomy.rb +331 -0
- data/lib/bio/db/lasergene.rb +209 -0
- data/lib/bio/db/litdb.rb +3 -27
- data/lib/bio/db/medline.rb +228 -249
- data/lib/bio/db/nbrf.rb +3 -3
- data/lib/bio/db/newick.rb +510 -0
- data/lib/bio/db/nexus.rb +1854 -0
- data/lib/bio/db/pdb.rb +5 -17
- data/lib/bio/db/pdb/atom.rb +2 -18
- data/lib/bio/db/pdb/chain.rb +2 -18
- data/lib/bio/db/pdb/chemicalcomponent.rb +2 -18
- data/lib/bio/db/pdb/model.rb +2 -18
- data/lib/bio/db/pdb/pdb.rb +73 -34
- data/lib/bio/db/pdb/residue.rb +4 -20
- data/lib/bio/db/pdb/utils.rb +2 -18
- data/lib/bio/db/prosite.rb +403 -422
- data/lib/bio/db/rebase.rb +84 -40
- data/lib/bio/db/soft.rb +404 -0
- data/lib/bio/db/transfac.rb +5 -17
- data/lib/bio/feature.rb +106 -52
- data/lib/bio/io/das.rb +32 -42
- data/lib/bio/io/dbget.rb +2 -20
- data/lib/bio/io/ddbjxml.rb +77 -138
- data/lib/bio/io/ebisoap.rb +158 -0
- data/lib/bio/io/ensembl.rb +229 -0
- data/lib/bio/io/fastacmd.rb +89 -82
- data/lib/bio/io/fetch.rb +163 -96
- data/lib/bio/io/flatfile.rb +170 -73
- data/lib/bio/io/flatfile/bdb.rb +3 -16
- data/lib/bio/io/flatfile/index.rb +2 -2
- data/lib/bio/io/flatfile/indexer.rb +3 -2
- data/lib/bio/io/higet.rb +12 -31
- data/lib/bio/io/keggapi.rb +210 -269
- data/lib/bio/io/ncbisoap.rb +155 -0
- data/lib/bio/io/pubmed.rb +169 -147
- data/lib/bio/io/registry.rb +4 -20
- data/lib/bio/io/soapwsdl.rb +43 -38
- data/lib/bio/io/sql.rb +242 -305
- data/lib/bio/location.rb +407 -285
- data/lib/bio/map.rb +410 -0
- data/lib/bio/pathway.rb +558 -695
- data/lib/bio/reference.rb +272 -75
- data/lib/bio/sequence.rb +255 -13
- data/lib/bio/sequence/aa.rb +71 -10
- data/lib/bio/sequence/common.rb +187 -33
- data/lib/bio/sequence/compat.rb +59 -4
- data/lib/bio/sequence/format.rb +54 -7
- data/lib/bio/sequence/generic.rb +3 -3
- data/lib/bio/sequence/na.rb +328 -26
- data/lib/bio/shell.rb +11 -4
- data/lib/bio/shell/core.rb +221 -160
- data/lib/bio/shell/demo.rb +18 -15
- data/lib/bio/shell/interface.rb +14 -12
- data/lib/bio/shell/irb.rb +95 -0
- data/lib/bio/shell/object.rb +45 -26
- data/lib/bio/shell/plugin/blast.rb +42 -0
- data/lib/bio/shell/plugin/codon.rb +22 -14
- data/lib/bio/shell/plugin/das.rb +58 -0
- data/lib/bio/shell/plugin/emboss.rb +2 -2
- data/lib/bio/shell/plugin/entry.rb +22 -11
- data/lib/bio/shell/plugin/flatfile.rb +2 -2
- data/lib/bio/shell/plugin/keggapi.rb +13 -6
- data/lib/bio/shell/plugin/midi.rb +4 -4
- data/lib/bio/shell/plugin/obda.rb +2 -2
- data/lib/bio/shell/plugin/psort.rb +56 -0
- data/lib/bio/shell/plugin/seq.rb +35 -8
- data/lib/bio/shell/plugin/soap.rb +87 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/bioruby_generator.rb +29 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_classes.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_log.rhtml +27 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_methods.rhtml +11 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_modules.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_variables.rhtml +7 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-bg.gif +0 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-console.png +0 -0
- data/lib/bio/shell/rails/{public/images/icon.png → vendor/plugins/generators/bioruby/templates/bioruby-gem.png} +0 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-link.gif +0 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby.css +369 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby.rhtml +47 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby_controller.rb +144 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby_helper.rb +47 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/commands.rhtml +8 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/history.rhtml +10 -0
- data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/index.rhtml +22 -0
- data/lib/bio/shell/script.rb +25 -0
- data/lib/bio/shell/setup.rb +109 -0
- data/lib/bio/shell/web.rb +70 -58
- data/lib/bio/tree.rb +850 -0
- data/lib/bio/util/color_scheme.rb +84 -107
- data/lib/bio/util/color_scheme/buried.rb +5 -24
- data/lib/bio/util/color_scheme/helix.rb +5 -24
- data/lib/bio/util/color_scheme/hydropathy.rb +5 -24
- data/lib/bio/util/color_scheme/nucleotide.rb +5 -24
- data/lib/bio/util/color_scheme/strand.rb +5 -24
- data/lib/bio/util/color_scheme/taylor.rb +5 -24
- data/lib/bio/util/color_scheme/turn.rb +5 -24
- data/lib/bio/util/color_scheme/zappo.rb +5 -24
- data/lib/bio/util/contingency_table.rb +70 -43
- 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 +4 -22
- data/sample/color_scheme_na.rb +4 -12
- data/sample/enzymes.rb +78 -0
- data/sample/goslim.rb +5 -13
- data/sample/psortplot_html.rb +4 -12
- data/test/data/blast/2.2.15.blastp.m7 +876 -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/iprscan/merged.raw +32 -0
- data/test/data/iprscan/merged.txt +74 -0
- data/test/data/soft/GDS100_partial.soft +92 -0
- data/test/data/soft/GSE3457_family_partial.soft +874 -0
- data/test/functional/bio/io/test_ensembl.rb +103 -0
- data/test/functional/bio/io/test_soapwsdl.rb +5 -17
- data/test/unit/bio/appl/bl2seq/test_report.rb +2 -2
- data/test/unit/bio/appl/blast/test_report.rb +3 -16
- data/test/unit/bio/appl/blast/test_xmlparser.rb +4 -16
- data/test/unit/bio/appl/genscan/test_report.rb +3 -16
- data/test/unit/bio/appl/hmmer/test_report.rb +3 -16
- 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 +3 -16
- data/test/unit/bio/appl/targetp/test_report.rb +3 -16
- data/test/unit/bio/appl/test_blast.rb +3 -16
- data/test/unit/bio/appl/test_fasta.rb +4 -16
- data/test/unit/bio/appl/test_pts1.rb +140 -0
- data/test/unit/bio/appl/tmhmm/test_report.rb +3 -16
- data/test/unit/bio/data/test_aa.rb +4 -17
- data/test/unit/bio/data/test_codontable.rb +3 -16
- data/test/unit/bio/data/test_na.rb +3 -3
- data/test/unit/bio/db/embl/test_common.rb +3 -16
- data/test/unit/bio/db/embl/test_embl.rb +3 -16
- data/test/unit/bio/db/embl/test_embl_rel89.rb +219 -0
- data/test/unit/bio/db/embl/test_sptr.rb +1548 -41
- data/test/unit/bio/db/embl/test_uniprot.rb +3 -16
- data/test/unit/bio/db/kegg/test_genes.rb +3 -16
- data/test/unit/bio/db/pdb/test_pdb.rb +7 -24
- data/test/unit/bio/db/test_aaindex.rb +2 -2
- data/test/unit/bio/db/test_fasta.rb +3 -16
- data/test/unit/bio/db/test_gff.rb +3 -16
- data/test/unit/bio/db/test_lasergene.rb +95 -0
- data/test/unit/bio/db/test_newick.rb +56 -0
- data/test/unit/bio/db/test_nexus.rb +360 -0
- data/test/unit/bio/db/test_prosite.rb +5 -18
- data/test/unit/bio/db/test_rebase.rb +11 -25
- data/test/unit/bio/db/test_soft.rb +138 -0
- data/test/unit/bio/io/test_ddbjxml.rb +5 -17
- data/test/unit/bio/io/test_ensembl.rb +109 -0
- data/test/unit/bio/io/test_fastacmd.rb +3 -16
- data/test/unit/bio/io/test_flatfile.rb +237 -0
- data/test/unit/bio/io/test_soapwsdl.rb +4 -17
- data/test/unit/bio/sequence/test_aa.rb +3 -3
- data/test/unit/bio/sequence/test_common.rb +3 -16
- data/test/unit/bio/sequence/test_compat.rb +3 -16
- data/test/unit/bio/sequence/test_na.rb +29 -3
- data/test/unit/bio/shell/plugin/test_seq.rb +8 -8
- data/test/unit/bio/test_alignment.rb +16 -27
- data/test/unit/bio/test_command.rb +242 -25
- data/test/unit/bio/test_db.rb +3 -16
- data/test/unit/bio/test_feature.rb +4 -16
- data/test/unit/bio/test_location.rb +4 -16
- data/test/unit/bio/test_map.rb +230 -0
- data/test/unit/bio/test_pathway.rb +4 -16
- data/test/unit/bio/test_reference.rb +2 -2
- data/test/unit/bio/test_sequence.rb +7 -19
- data/test/unit/bio/test_shell.rb +3 -16
- 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 +100 -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 +6 -18
- data/test/unit/bio/util/test_contingency_table.rb +6 -18
- data/test/unit/bio/util/test_restriction_enzyme.rb +42 -0
- data/test/unit/bio/util/test_sirna.rb +3 -16
- metadata +228 -169
- data/doc/BioRuby.rd.ja +0 -225
- data/doc/Design.rd.ja +0 -341
- data/doc/TODO.rd.ja +0 -138
- data/lib/bio/appl/fasta/format6.rb +0 -37
- data/lib/bio/db/kegg/cell.rb +0 -88
- data/lib/bio/db/kegg/ko.rb +0 -178
- data/lib/bio/shell/rails/Rakefile +0 -10
- data/lib/bio/shell/rails/app/controllers/application.rb +0 -4
- data/lib/bio/shell/rails/app/controllers/shell_controller.rb +0 -94
- data/lib/bio/shell/rails/app/helpers/application_helper.rb +0 -3
- data/lib/bio/shell/rails/app/models/shell_connection.rb +0 -30
- data/lib/bio/shell/rails/app/views/layouts/shell.rhtml +0 -37
- data/lib/bio/shell/rails/app/views/shell/history.rhtml +0 -5
- data/lib/bio/shell/rails/app/views/shell/index.rhtml +0 -2
- data/lib/bio/shell/rails/app/views/shell/show.rhtml +0 -13
- data/lib/bio/shell/rails/config/boot.rb +0 -19
- data/lib/bio/shell/rails/config/database.yml +0 -85
- data/lib/bio/shell/rails/config/environment.rb +0 -53
- data/lib/bio/shell/rails/config/environments/development.rb +0 -19
- data/lib/bio/shell/rails/config/environments/production.rb +0 -19
- data/lib/bio/shell/rails/config/environments/test.rb +0 -19
- data/lib/bio/shell/rails/config/routes.rb +0 -19
- data/lib/bio/shell/rails/doc/README_FOR_APP +0 -2
- data/lib/bio/shell/rails/public/404.html +0 -8
- data/lib/bio/shell/rails/public/500.html +0 -8
- data/lib/bio/shell/rails/public/dispatch.cgi +0 -10
- data/lib/bio/shell/rails/public/dispatch.fcgi +0 -24
- data/lib/bio/shell/rails/public/dispatch.rb +0 -10
- data/lib/bio/shell/rails/public/favicon.ico +0 -0
- data/lib/bio/shell/rails/public/images/rails.png +0 -0
- data/lib/bio/shell/rails/public/index.html +0 -277
- data/lib/bio/shell/rails/public/javascripts/controls.js +0 -750
- data/lib/bio/shell/rails/public/javascripts/dragdrop.js +0 -584
- data/lib/bio/shell/rails/public/javascripts/effects.js +0 -854
- data/lib/bio/shell/rails/public/javascripts/prototype.js +0 -1785
- data/lib/bio/shell/rails/public/robots.txt +0 -1
- data/lib/bio/shell/rails/public/stylesheets/main.css +0 -187
- data/lib/bio/shell/rails/script/about +0 -3
- data/lib/bio/shell/rails/script/breakpointer +0 -3
- data/lib/bio/shell/rails/script/console +0 -3
- data/lib/bio/shell/rails/script/destroy +0 -3
- data/lib/bio/shell/rails/script/generate +0 -3
- data/lib/bio/shell/rails/script/performance/benchmarker +0 -3
- data/lib/bio/shell/rails/script/performance/profiler +0 -3
- data/lib/bio/shell/rails/script/plugin +0 -3
- data/lib/bio/shell/rails/script/process/reaper +0 -3
- data/lib/bio/shell/rails/script/process/spawner +0 -3
- data/lib/bio/shell/rails/script/process/spinner +0 -3
- data/lib/bio/shell/rails/script/runner +0 -3
- data/lib/bio/shell/rails/script/server +0 -42
- data/lib/bio/shell/rails/test/test_helper.rb +0 -28
data/doc/KEGG_API.rd.ja
CHANGED
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=begin
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$Id: KEGG_API.rd.ja,v 1.
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$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 �λȤ���>))
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* ((<Ruby ��>))
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* ((<Perl ��>))
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22
|
+
* ((<Perl ��������>))
|
22
23
|
* ((<Python ��>))
|
23
24
|
* ((<Java ��>))
|
24
25
|
* ((<KEGG API ��ե����>))
|
@@ -30,76 +31,96 @@ KEGG API
|
|
30
31
|
* ((<Definition ��>)), ((<ArrayOfDefinition ��>))
|
31
32
|
* ((<LinkDBRelation ��>)), ((<ArrayOfLinkDBRelation ��>))
|
32
33
|
* ((<PathwayElement ��>)), ((<ArrayOfPathwayElement ��>))
|
34
|
+
* ((<PathwayElementRelation ��>)), ((<ArrayOfPathwayElementRelation ��>))
|
35
|
+
* ((<Subtype ��>)), ((<ArrayOfSubtype ��>))
|
36
|
+
* ((<StructureAlignment ��>)), ((<ArrayOfStructureAlignment ��>))
|
33
37
|
* ((<��åɰ���>))
|
34
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|
* ((<�����>))
|
35
|
-
* ((<list_databases>))
|
36
|
-
|
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-
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+
* ((<list_databases>))
|
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+
* ((<list_organisms>))
|
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+
* ((<list_pathways>))
|
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* ((<DBGET>))
|
39
|
-
* ((<binfo>))
|
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|
-
|
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-
|
42
|
-
|
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-
|
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+
* ((<binfo>))
|
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+
* ((<bfind>))
|
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+
* ((<bget>))
|
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+
* ((<btit>))
|
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|
+
* ((<bconv>))
|
44
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|
* ((<LinkDB>))
|
45
|
-
* ((
|
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-
|
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-
((<
|
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|
-
* ((
|
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-
((<
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-
((<
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-
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-
((<
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-
((<
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-
((<
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|
-
((<
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-
((<
|
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|
-
((<
|
49
|
+
* ((<�ǡ����١����֤Υ��>))
|
50
|
+
* ((<get_linkdb_by_entry>))
|
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|
+
* ((<get_linkdb_between_databases>))
|
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+
* ((<�����Ҥȹ����ֹ�δط�>))
|
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+
* ((<get_genes_by_enzyme>))
|
54
|
+
* ((<get_enzymes_by_gene>))
|
55
|
+
* ((<���ǡ�����ʪ���ꥢ�������δط�>))
|
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+
* ((<get_enzymes_by_compound>))
|
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+
* ((<get_enzymes_by_glycan>))
|
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+
* ((<get_enzymes_by_reaction>))
|
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+
* ((<get_compounds_by_enzyme>))
|
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+
* ((<get_compounds_by_reaction>))
|
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+
* ((<get_glycans_by_enzyme>))
|
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+
* ((<get_glycans_by_reaction>))
|
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+
* ((<get_reactions_by_enzyme>))
|
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+
* ((<get_reactions_by_compound>))
|
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+
* ((<get_reactions_by_glycan>))
|
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|
* ((<SSDB>))
|
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|
-
* ((<get_best_best_neighbors_by_gene>))
|
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-
|
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-
|
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-
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-
# * ((<get_neighbors_by_gene>)),
|
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|
-
# ((<get_similarity_between_genes>))
|
67
|
+
* ((<get_best_best_neighbors_by_gene>))
|
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|
+
* ((<get_best_neighbors_by_gene>))
|
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|
+
* ((<get_reverse_best_neighbors_by_gene>))
|
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|
+
* ((<get_paralogs_by_gene>))
|
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|
* ((<Motif>))
|
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|
-
* ((<get_motifs_by_gene>))
|
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|
-
|
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|
-
* ((<KO
|
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|
-
* ((<get_ko_by_gene>))
|
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|
-
|
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|
-
|
72
|
-
|
73
|
-
((<get_oc_members_by_gene>)),
|
74
|
-
((<get_pc_members_by_gene>))
|
75
|
-
# ((<get_ko_members>)),
|
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>))
|
76
79
|
* ((<PATHWAY>))
|
77
|
-
* ((
|
78
|
-
((<
|
79
|
-
((<
|
80
|
-
((<
|
81
|
-
((<
|
82
|
-
((<
|
83
|
-
|
84
|
-
|
85
|
-
((<
|
86
|
-
|
87
|
-
((<
|
88
|
-
((<
|
89
|
-
((<
|
90
|
-
|
91
|
-
((<
|
92
|
-
((<
|
93
|
-
((<
|
94
|
-
|
95
|
-
((<
|
96
|
-
|
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>))
|
97
106
|
* ((<GENES>))
|
98
107
|
* ((<get_genes_by_organism>))
|
99
108
|
* ((<GENOME>))
|
100
109
|
* ((<get_number_of_genes_by_organism>))
|
101
110
|
* ((<LIGAND>))
|
102
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>))
|
103
124
|
|
104
125
|
== ����ȥ����������
|
105
126
|
|
@@ -162,13 +183,13 @@ XML
|
|
162
183
|
require 'soap/wsdlDriver'
|
163
184
|
|
164
185
|
wsdl = "http://soap.genome.jp/KEGG.wsdl"
|
165
|
-
serv = SOAP::WSDLDriverFactory.new(wsdl).
|
186
|
+
serv = SOAP::WSDLDriverFactory.new(wsdl).create_rpc_driver
|
166
187
|
serv.generate_explicit_type = true # SOAP �� Ruby �η��Ѵ���ͭ���ˤ���
|
167
188
|
|
168
|
-
|
169
|
-
|
189
|
+
offset = 1
|
190
|
+
limit = 5
|
170
191
|
|
171
|
-
top5 = serv.get_best_neighbors_by_gene('eco:b0002',
|
192
|
+
top5 = serv.get_best_neighbors_by_gene('eco:b0002', offset, limit)
|
172
193
|
top5.each do |hit|
|
173
194
|
print hit.genes_id1, "\t", hit.genes_id2, "\t", hit.sw_score, "\n"
|
174
195
|
end
|
@@ -185,7 +206,7 @@ XML
|
|
185
206
|
|
186
207
|
���ޤ�ư���ʤ����ϡ�
|
187
208
|
|
188
|
-
serv = SOAP::WSDLDriverFactory.new(wsdl).
|
209
|
+
serv = SOAP::WSDLDriverFactory.new(wsdl).create_rpc_driver
|
189
210
|
serv.wiredump_dev = STDERR # �����ιԤ����
|
190
211
|
serv.generate_explicit_type = true
|
191
212
|
|
@@ -193,28 +214,30 @@ XML
|
|
193
214
|
�����ФȤΤ���꤬ɸ�२�顼�˽��Ϥ���ޤ���
|
194
215
|
|
195
216
|
KEGG API v3.0 ���顢�����Ф���ô��ڤ���������ॢ���Ȥ��ɤ���Ū�ǡ�
|
196
|
-
���̤η�̤��֤���åɤˤ�
|
197
|
-
|
198
|
-
|
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���
|
199
222
|
|
200
223
|
#!/usr/bin/env ruby
|
201
224
|
|
202
225
|
require 'soap/wsdlDriver'
|
203
226
|
|
204
227
|
wsdl = "http://soap.genome.jp/KEGG.wsdl"
|
205
|
-
serv = SOAP::WSDLDriverFactory.new(wsdl).
|
228
|
+
serv = SOAP::WSDLDriverFactory.new(wsdl).create_rpc_driver
|
206
229
|
serv.generate_explicit_type = true
|
207
230
|
|
208
|
-
|
209
|
-
|
231
|
+
offset = 1
|
232
|
+
limit = 100
|
210
233
|
|
211
234
|
loop do
|
212
|
-
results = serv.get_best_neighbors_by_gene('eco:b0002',
|
235
|
+
results = serv.get_best_neighbors_by_gene('eco:b0002', offset, limit)
|
213
236
|
break unless results # ��̤��֤äƤ��ʤ���н�λ
|
214
237
|
results.each do |hit|
|
215
238
|
print hit.genes_id1, "\t", hit.genes_id2, "\t", hit.sw_score, "\n"
|
216
239
|
end
|
217
|
-
|
240
|
+
offset += limit
|
218
241
|
end
|
219
242
|
|
220
243
|
WSDL ���Ѥ��Ƥ��뤿�ᡢ��������Ǥ� Ruby �ξ��Ͻ�ʬ�˴�ñ�˽�
|
@@ -299,7 +322,8 @@ sw_score
|
|
299
322
|
|
300
323
|
Perl �Ǥϡ��ʲ��Υ饤�֥����ɲå��ȡ��뤷�Ƥ���ɬ�פ�����ޤ���
|
301
324
|
|
302
|
-
* ((<SOAP::Lite|URL://soaplite.com/>))
|
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�
|
303
327
|
* ((<MIME-Base64|URL:http://search.cpan.org/author/GAAS/MIME-Base64/>))
|
304
328
|
* ((<libwww-perl|URL:http://search.cpan.org/author/GAAS/libwww-perl/>))
|
305
329
|
* ((<URI|URL:http://search.cpan.org/author/GAAS/URI/>))
|
@@ -314,10 +338,10 @@ Perl
|
|
314
338
|
|
315
339
|
$serv = SOAP::Lite -> service($wsdl);
|
316
340
|
|
317
|
-
$
|
318
|
-
$
|
341
|
+
$offset = 1;
|
342
|
+
$limit = 5;
|
319
343
|
|
320
|
-
$top5 = $serv->get_best_neighbors_by_gene('eco:b0002', $
|
344
|
+
$top5 = $serv->get_best_neighbors_by_gene('eco:b0002', $offset, $limit);
|
321
345
|
|
322
346
|
foreach $hit (@{$top5}) {
|
323
347
|
print "$hit->{genes_id1}\t$hit->{genes_id2}\t$hit->{sw_score}\n";
|
@@ -362,6 +386,74 @@ SOAP::Lite
|
|
362
386
|
|
363
387
|
�Τ褦�ˤʤ�ޤ���
|
364
388
|
|
389
|
+
=== Perl ��������
|
390
|
+
|
391
|
+
KEGG API �ˤ�ʸ�������ͤ����������˼���åɤ������Ĥ�����ޤ�����
|
392
|
+
���Ѥ��� SOAP::Lite �ΥС������˱����ơ�ɬ���ʲ��Τɤ��餫���н褬ɬ�פǤ���
|
393
|
+
|
394
|
+
==== SOAP::Lite v0.60 �ޤ�
|
395
|
+
|
396
|
+
Perl ������ (array) ���֥������Ȥ�����Ȥ��� KEGG API ���Ϥ����ϡ�
|
397
|
+
ɬ���ʲ��Τ褦�� SOAP ���֥������Ȥ�����Ū���Ѵ�����ɬ�פ�����ޤ���
|
398
|
+
|
399
|
+
SOAP::Data->type(array => [value1, value2, ... ])
|
400
|
+
|
401
|
+
==== SOAP::Lite v0.61 �ʹ�
|
402
|
+
|
403
|
+
SOAP::Lite v0.68 �ޤǤϥХ�������ޤ��Τ� v0.69 �ʹߤ����Ѥ��ᤷ�ޤ���
|
404
|
+
|
405
|
+
Perl ��ʸ���� (string) ����� (int) ������ (array) ���֥������Ȥ�
|
406
|
+
ArrayOfstring �� ArrayOfint ���� SOAP ���֥������Ȥ��Ѵ�����
|
407
|
+
���֥롼����������ɲä���ɬ�פ�����ޤ���
|
408
|
+
|
409
|
+
sub SOAP::Serializer::as_ArrayOfstring{
|
410
|
+
my ($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
|
+
}
|
365
457
|
|
366
458
|
=== Python ��
|
367
459
|
|
@@ -385,7 +477,6 @@ Python
|
|
385
477
|
results = serv.get_genes_by_pathway('path:eco00020')
|
386
478
|
print results
|
387
479
|
|
388
|
-
|
389
480
|
=== Java ��
|
390
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|
|
391
482
|
Java �Ǥ� Apache Axis �饤�֥��� axis-1.2alpha ��꿷�����С������
|
@@ -485,7 +576,6 @@ tcsh
|
|
485
576
|
|
486
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|
* ((<URL:http://www.genome.jp/kegg/soap/doc/keggapi_javadoc_ja/>))
|
487
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|
|
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|
-
|
489
579
|
== KEGG API ��ե����
|
490
580
|
|
491
581
|
�ʲ��Ǥϡ�KEGG API ��Ȥ��Τ�ɬ�פʾ�������ƤΥ�åɤ���⤷�ޤ���
|
@@ -517,7 +607,7 @@ URL
|
|
517
607
|
* entry_id �� db_name �ȥ���ȥ�̾�� ':' �Ƿ�礷�����ƤΥǡ����١����֤�
|
518
608
|
��ˡ����� ID �Ǥ������Ȥ��� embl:J00231 �� EMBL �Υ���ȥ� J00231 ��
|
519
609
|
�ؤ��ޤ���entry_id �ϡ��ʲ��� genes_id, enzyme_id, compound_id,
|
520
|
-
glycan_id, reaction_id, pathway_id, motif_id �ʤɤ�ޤߤޤ���
|
610
|
+
drug_id, glycan_id, reaction_id, pathway_id, motif_id �ʤɤ�ޤߤޤ���
|
521
611
|
|
522
612
|
* genes_id �� keggorg �Ȱ�����̾�� ':' �Ƿ�礷�� KEGG �ΰ����� ID �Ǥ���
|
523
613
|
eco:b0001 ����IJ�ݤΰ����� b0001 ��ؤ��ޤ���
|
@@ -528,6 +618,9 @@ URL
|
|
528
618
|
* compound_id �� cpd: ��Ĥ�������ʪ�� ID �Ǥ���cpd:C00158 �ϲ���ʪ�ֹ�
|
529
619
|
C00158 �β���ʪ�Ǥ��륯�������ؤ��ޤ���
|
530
620
|
|
621
|
+
* drug_id �� dr: ��Ĥ�������ʪ�� ID �Ǥ���dr:D00201 �ϥɥ�å��ֹ�
|
622
|
+
D00201 �Υɥ�å��Ǥ���ƥȥ饵��������ؤ��ޤ���
|
623
|
+
|
531
624
|
* glycan_id �� gl: ��Ĥ�������ʪ�� ID �Ǥ���gl:G00050 �������ֹ�
|
532
625
|
G00050 �������Ǥ��� Paragloboside ��ؤ��ޤ���
|
533
626
|
|
@@ -555,9 +648,9 @@ URL
|
|
555
648
|
|
556
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|
* ((<URL:http://www.genome.jp/dbget-bin/get_htext?KO>))
|
557
650
|
|
558
|
-
*
|
559
|
-
|
560
|
-
|
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����֤�
|
561
654
|
��åɤ�ƤӤޤ���
|
562
655
|
|
563
656
|
* fg_color_list �ϥѥ��������ؤο��Ť��ǥ��֥������Ȥ��Ȥ�ʸ����������
|
@@ -566,6 +659,9 @@ URL
|
|
566
659
|
* fg_color_list �ϥѥ��������ؤο��Ť��ǥ��֥������Ȥ��Ȥ��طʤ�
|
567
660
|
������ꤹ������Ǥ���
|
568
661
|
|
662
|
+
��Ϣ URL��
|
663
|
+
* ((<URL:http://www.genome.jp/kegg/kegg3.html>))
|
664
|
+
|
569
665
|
=== ����ͤΥǡ�����
|
570
666
|
|
571
667
|
KEGG API �Υ�åɤ�ʸ����ʤ�ñ����ͤ��֤���Τ����Ǥʤ���ʣ���ʥǡ���
|
@@ -640,6 +736,8 @@ SSDB
|
|
640
736
|
|
641
737
|
+ PathwayElement ��
|
642
738
|
|
739
|
+
�ѥ����������������Ƥ���ġ���Ȣ��ݤʤɤΥ��֥������Ȥ�ɽ���ǡ������Ǥ���
|
740
|
+
|
643
741
|
element_id �ѥ���������Υ��֥������Ȥ�ؤ���ˡ����� ID (int)
|
644
742
|
type ���֥������Ȥμ��� ("gene", "enzyme" �ʤ�) (string)
|
645
743
|
names ���֥������ȤˤĤ���줿̾���Υꥹ�� (ArrayOfstring)
|
@@ -649,6 +747,46 @@ SSDB
|
|
649
747
|
|
650
748
|
ʣ���� PathwayElement ���ǡ�����ޤ�����Ǥ���
|
651
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���
|
652
790
|
|
653
791
|
=== ��åɰ���
|
654
792
|
|
@@ -660,7 +798,6 @@ KEGG API
|
|
660
798
|
�ʲ�����Ǥϡ������ʤɤ� Ruby �����ɽ������äƽ�Ƥ��ޤ������ºݤ�
|
661
799
|
�������ä˥ꥹ�Ȥ��Ϥ����ʤɡˤϻ��Ѥ������ˤ�äưۤʤ��ǽ��������ޤ���
|
662
800
|
|
663
|
-
|
664
801
|
==== �����
|
665
802
|
|
666
803
|
�ǿ��Υǡ����١�������ʤɤ��֤�����Υ�åɤǤ���
|
@@ -672,6 +809,10 @@ KEGG
|
|
672
809
|
���͡�
|
673
810
|
ArrayOfDefinition (db, definition)
|
674
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
|
+
|
675
816
|
--- list_organisms
|
676
817
|
|
677
818
|
���� KEGG �˴ޤޤ�Ƥ�����ʪ�� (org) �Υꥹ�Ȥ��֤��ޤ���
|
@@ -679,7 +820,11 @@ KEGG
|
|
679
820
|
���͡�
|
680
821
|
ArrayOfDefinition (org, definition)
|
681
822
|
|
682
|
-
|
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)
|
683
828
|
|
684
829
|
���� KEGG �˴ޤޤ�Ƥ�����ꤷ����ʪ�Υѥ��������Υꥹ�Ȥ��֤��ޤ���������
|
685
830
|
'map' �Ȥ���ʸ�����Ϳ����ȥ�ե���ѥ��������Υꥹ�Ȥ��֤��ޤ���
|
@@ -687,15 +832,19 @@ KEGG
|
|
687
832
|
���͡�
|
688
833
|
ArrayOfDefinition (pathway_id, definition)
|
689
834
|
|
835
|
+
��Ϣ URL��
|
836
|
+
* ((<URL:http://www.genome.jp/kegg/pathway.html>))
|
690
837
|
|
691
838
|
==== DBGET
|
692
839
|
|
693
840
|
DBGET �����ƥ���Ф����åɤΰ����Ǥ���DBGET �ˤĤ��ƾܤ����ϰʲ���
|
694
841
|
�ڡ����Ȥ��Ƥ���������
|
695
842
|
|
843
|
+
��Ϣ URL��
|
696
844
|
* ((<URL:http://www.genome.jp/dbget/dbget_manual.html>))
|
845
|
+
* ((<URL:http://www.genome.jp/dbget-bin/binfo>))
|
697
846
|
|
698
|
-
--- binfo(string)
|
847
|
+
--- binfo(string:db)
|
699
848
|
|
700
849
|
���ꤷ���ǡ����١����Υ���ȥ���乹�����ʤɾܤ����ǿ�������֤��ޤ���
|
701
850
|
'all' ���Ϥ������Ѳ�ǽ�����ƤΥǡ����١����ξ�����֤��ޤ���
|
@@ -710,7 +859,7 @@ binfo
|
|
710
859
|
# ���ƤΥǡ����١����κǿ�����
|
711
860
|
binfo('all')
|
712
861
|
|
713
|
-
--- bfind(string)
|
862
|
+
--- bfind(string:str)
|
714
863
|
|
715
864
|
DBGET �� bfind ���ޥ�ɤؤΥ�åѡ��Ǥ���������ɤˤ�ꥨ��ȥ��
|
716
865
|
�������뤳�Ȥ��Ǥ��ޤ������٤�Ϳ�����륭����ɤο��� 100 �İʲ���
|
@@ -724,7 +873,7 @@ DBGET
|
|
724
873
|
bfind("gb E-cadherin human")
|
725
874
|
|
726
875
|
|
727
|
-
--- bget(string)
|
876
|
+
--- bget(string:str)
|
728
877
|
|
729
878
|
���ꤷ�� entry_id �Υ���ȥ���֤��ޤ���GENES �ΰ����ҥ���ȥ��Ϥ��ᡢ
|
730
879
|
���Υ�ͥåȤ� DBGET �����ƥ������Ƥ����͡��ʥǡ����١���
|
@@ -743,7 +892,7 @@ DBGET
|
|
743
892
|
# FASTA �ե����ޥåȤα�����������
|
744
893
|
bget("-f -n n eco:b0002 hin:tRNA-Cys-1")
|
745
894
|
|
746
|
-
--- btit(string)
|
895
|
+
--- btit(string:str)
|
747
896
|
|
748
897
|
DBGET �� btit ���ޥ�ɤؤΥ�åѡ��Ǥ������ꤷ������ȥ�� ID ���б���
|
749
898
|
��ǥե��˥������֤��ޤ������٤�Ϳ�����륨��ȥ�ο��� 100 �İʲ���
|
@@ -756,11 +905,25 @@ DBGET
|
|
756
905
|
# ����飴�Ĥΰ����ҤΥǥե��˥�����
|
757
906
|
btit("hsa:1798 mmu:13478 dme:CG5287-PA cel:Y60A3A.14")
|
758
907
|
|
759
|
-
--- bconv(string)
|
908
|
+
--- bconv(string:str)
|
760
909
|
|
761
|
-
�����ǡ����١����� ID �� KEGG �� ID
|
762
|
-
�١����� NCBI Gene ID, NCBI GI, GenBank ID, UniProt ID �Ǥ���
|
910
|
+
�����ǡ����١����� ID �� KEGG �� ID ���Ѵ����ޤ���
|
763
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���
|
764
927
|
|
765
928
|
���͡�
|
766
929
|
string
|
@@ -769,9 +932,14 @@ DBGET
|
|
769
932
|
# NCBI GI �� Gene ID �� KEGG genes_id ���Ѵ�
|
770
933
|
serv.bconv("ncbi-gi:10047086 ncbi-gi:10047090 ncbi-geneid:14751")
|
771
934
|
|
935
|
+
��Ϣ URL��
|
936
|
+
* ((<URL:http://www.genome.jp/kegg/genes.html>)) (Gene name conversion)
|
937
|
+
|
772
938
|
==== LinkDB
|
773
939
|
|
774
|
-
|
940
|
+
+ �ǡ����١����֤Υ��
|
941
|
+
|
942
|
+
--- get_linkdb_by_entry(string:entry_id, string:db, int:offset, int:limit)
|
775
943
|
|
776
944
|
���ꤷ�� entry_id ����ľ�ܤޤ��ϴ���Ū�˥����Ƥ��륨��ȥ�η�ϩ��
|
777
945
|
db �ǻ��ꤷ���ǡ����١����ˤ��ɤ��ޤǸ������ޤ���
|
@@ -784,9 +952,35 @@ db
|
|
784
952
|
get_linkdb_by_entry('eco:b0002', 'pathway', 1, 10)
|
785
953
|
get_linkdb_by_entry('eco:b0002', 'pathway', 11, 10)
|
786
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
|
+
|
787
981
|
+ �����Ҥȹ����ֹ�δط�
|
788
982
|
|
789
|
-
--- get_genes_by_enzyme(enzyme_id, org)
|
983
|
+
--- get_genes_by_enzyme(string:enzyme_id, string:org)
|
790
984
|
|
791
985
|
�о���ʪ��ˤ����ơ����ꤷ�������ֹ����İ����ҤΥꥹ�Ȥ��֤��ޤ���
|
792
986
|
|
@@ -797,7 +991,7 @@ db
|
|
797
991
|
# �����ֹ� 1.1.1.1 �������IJ�ݤΰ����ҤΥꥹ��
|
798
992
|
get_genes_by_enzyme('ec:1.1.1.1', 'eco')
|
799
993
|
|
800
|
-
--- get_enzymes_by_gene(genes_id)
|
994
|
+
--- get_enzymes_by_gene(string:genes_id)
|
801
995
|
|
802
996
|
���ꤷ�������Ҥ��б���������ֹ�Υꥹ�Ȥ��֤��ޤ���
|
803
997
|
|
@@ -808,10 +1002,9 @@ db
|
|
808
1002
|
# ��IJ�ݰ����� 'eco:b0002' �ι����ֹ�Υꥹ��
|
809
1003
|
get_enzymes_by_gene(eco:b0002)
|
810
1004
|
|
811
|
-
|
812
1005
|
+ ���ǡ�����ʪ���ꥢ�������δط�
|
813
1006
|
|
814
|
-
--- get_enzymes_by_compound(compound_id)
|
1007
|
+
--- get_enzymes_by_compound(string:compound_id)
|
815
1008
|
|
816
1009
|
���ꤷ������ʪ���б���������ֹ�Υꥹ�Ȥ��֤��ޤ���
|
817
1010
|
|
@@ -822,7 +1015,7 @@ db
|
|
822
1015
|
# ����ʪ 'cpd:C00345' ����դ˴ؤ����ǤΥꥹ��
|
823
1016
|
get_enzymes_by_compound('cpd:C00345')
|
824
1017
|
|
825
|
-
--- get_enzymes_by_glycan(compound_id)
|
1018
|
+
--- get_enzymes_by_glycan(string:compound_id)
|
826
1019
|
|
827
1020
|
���ꤷ���������б���������ֹ�Υꥹ�Ȥ��֤��ޤ���
|
828
1021
|
|
@@ -833,7 +1026,7 @@ db
|
|
833
1026
|
# ���� 'gl:G00001' ����դ˴ؤ����ǤΥꥹ��
|
834
1027
|
get_enzymes_by_glycan('gl:G00001')
|
835
1028
|
|
836
|
-
--- get_enzymes_by_reaction(reaction_id)
|
1029
|
+
--- get_enzymes_by_reaction(string:reaction_id)
|
837
1030
|
|
838
1031
|
���ꤷ���ꥢ��������ֹ���б���������ֹ�Υꥹ�Ȥ��֤��ޤ���
|
839
1032
|
|
@@ -844,7 +1037,7 @@ db
|
|
844
1037
|
# �ꥢ��������ֹ� R00100 ����Ĺ��ǤΥꥹ��
|
845
1038
|
get_enzymes_by_reaction('rn:R00100')
|
846
1039
|
|
847
|
-
--- get_compounds_by_enzyme(enzyme_id)
|
1040
|
+
--- get_compounds_by_enzyme(string:enzyme_id)
|
848
1041
|
|
849
1042
|
���ꤷ�������ֹ���б����벽��ʪ�Υꥹ�Ȥ��֤��ޤ���
|
850
1043
|
|
@@ -855,7 +1048,7 @@ db
|
|
855
1048
|
# �����ֹ� 'ec:2.7.1.12' ����դ˴ؤ�벽��ʪ�Υꥹ��
|
856
1049
|
get_compounds_by_enzyme('ec:2.7.1.12')
|
857
1050
|
|
858
|
-
--- get_compounds_by_reaction(reaction_id)
|
1051
|
+
--- get_compounds_by_reaction(string:reaction_id)
|
859
1052
|
|
860
1053
|
���ꤷ���ꥢ���������б����벽��ʪ�Υꥹ�Ȥ��֤��ޤ���
|
861
1054
|
|
@@ -866,7 +1059,7 @@ db
|
|
866
1059
|
# �ꥢ��������ֹ� 'rn:R00100' ��ȿ���˴ؤ�벽��ʪ�Υꥹ��
|
867
1060
|
get_compounds_by_reaction('rn:R00100')
|
868
1061
|
|
869
|
-
--- get_glycans_by_enzyme(enzyme_id)
|
1062
|
+
--- get_glycans_by_enzyme(string:enzyme_id)
|
870
1063
|
|
871
1064
|
���ꤷ�������ֹ���б����������Υꥹ�Ȥ��֤��ޤ���
|
872
1065
|
|
@@ -877,7 +1070,7 @@ db
|
|
877
1070
|
# �����ֹ� 'ec:2.4.1.141' ����դ˴ؤ�������Υꥹ��
|
878
1071
|
get_glycans_by_enzyme('ec:2.4.1.141')
|
879
1072
|
|
880
|
-
--- get_glycans_by_reaction(reaction_id)
|
1073
|
+
--- get_glycans_by_reaction(string:reaction_id)
|
881
1074
|
|
882
1075
|
���ꤷ���ꥢ���������б����������Υꥹ�Ȥ��֤��ޤ���
|
883
1076
|
|
@@ -888,7 +1081,7 @@ db
|
|
888
1081
|
# �ꥢ��������ֹ� 'rn:R06164' ��ȿ���˴ؤ�������Υꥹ��
|
889
1082
|
get_glycans_by_reaction('rn:R06164')
|
890
1083
|
|
891
|
-
--- get_reactions_by_enzyme(enzyme_id)
|
1084
|
+
--- get_reactions_by_enzyme(string:enzyme_id)
|
892
1085
|
|
893
1086
|
���ꤷ�������ֹ���б�����ꥢ�������Υꥹ�Ȥ��֤��ޤ���
|
894
1087
|
|
@@ -899,7 +1092,7 @@ db
|
|
899
1092
|
# �����ֹ� 'ec:2.7.1.12' ��ȿ���˴ؤ��ꥢ��������ֹ�Υꥹ��
|
900
1093
|
get_reactions_by_enzyme('ec:2.7.1.12')
|
901
1094
|
|
902
|
-
--- get_reactions_by_compound(compound_id)
|
1095
|
+
--- get_reactions_by_compound(string:compound_id)
|
903
1096
|
|
904
1097
|
���ꤷ������ʪ���б�����ꥢ�������Υꥹ�Ȥ��֤��ޤ���
|
905
1098
|
|
@@ -910,7 +1103,7 @@ db
|
|
910
1103
|
# ����ʪ 'cpd:C00199' �ο���ȿ���˴ؤ��ꥢ��������ֹ�Υꥹ��
|
911
1104
|
get_reactions_by_compound('cpd:C00199')
|
912
1105
|
|
913
|
-
--- get_reactions_by_glycan(glycan_id)
|
1106
|
+
--- get_reactions_by_glycan(string:glycan_id)
|
914
1107
|
|
915
1108
|
���ꤷ���������б�����ꥢ�������Υꥹ�Ȥ��֤��ޤ���
|
916
1109
|
|
@@ -921,7 +1114,6 @@ db
|
|
921
1114
|
# ���� 'gl:G00001' �ο���ȿ���˴ؤ��ꥢ��������ֹ�Υꥹ��
|
922
1115
|
get_reactions_by_glycan('gl:G00001')
|
923
1116
|
|
924
|
-
|
925
1117
|
==== SSDB
|
926
1118
|
|
927
1119
|
SSDB �ǡ����١������Ф����åɤΰ����Ǥ���SSDB �� KEGG/GENES �˴ޤޤ��
|
@@ -937,22 +1129,8 @@ SSDB
|
|
937
1129
|
|
938
1130
|
* ((<URL:http://www.genome.jp/kegg/ssdb/>))
|
939
1131
|
|
940
|
-
#--- get_neighbors_by_gene(genes_id, org, start, max_results)
|
941
|
-
#
|
942
|
-
#���ꤷ�� genes_id �ΰ����Ҥ˥ۥ�������Τ����������Ҥ���ꤷ����ʪ����
|
943
|
-
#�������ޤ����ޤ� org �� 'all' ����ꤹ�������ʪ�狼�鸡�����ޤ���
|
944
|
-
#
|
945
|
-
#���͡�
|
946
|
-
# ArrayOfSSDBRelation
|
947
|
-
#
|
948
|
-
#�㡧
|
949
|
-
# # ��IJ�ݤΰ����� b0002 ����Ʊ���Τ�������Ҥ����Ƹ������ơ���̤Σ���
|
950
|
-
# # ���飱�����ܤޤǤ��֤��ޤ�
|
951
|
-
# get_neighbors_by_gene('eco:b0002', 'all' 1, 10)
|
952
|
-
# # ���Σ����Ĥ� start = start + max_results �Ȥ��Ƽ��ޤ�
|
953
|
-
# get_neighbors_by_gene('eco:b0002', 'all' 11, 10)
|
954
1132
|
|
955
|
-
--- get_best_best_neighbors_by_gene(genes_id,
|
1133
|
+
--- get_best_best_neighbors_by_gene(string:genes_id, int:offset, int:limit)
|
956
1134
|
|
957
1135
|
������ȥ������åȤ� best-best �δط��ˤ�������Ҥ��������ޤ���
|
958
1136
|
|
@@ -964,7 +1142,7 @@ SSDB
|
|
964
1142
|
get_best_best_neighbors_by_gene('eco:b0002', 1, 10)
|
965
1143
|
get_best_best_neighbors_by_gene('eco:b0002', 11, 10)
|
966
1144
|
|
967
|
-
--- get_best_neighbors_by_gene(genes_id,
|
1145
|
+
--- get_best_neighbors_by_gene(string:genes_id, int:offset, int:limit)
|
968
1146
|
|
969
1147
|
�����꤫�鸫�ƥ٥��ȥҥåȤδط��ˤ�������Ҥ��������ޤ���
|
970
1148
|
|
@@ -976,7 +1154,7 @@ SSDB
|
|
976
1154
|
get_best_neighbors_by_gene('eco:b0002', 1, 10)
|
977
1155
|
get_best_neighbors_by_gene('eco:b0002', 11, 10)
|
978
1156
|
|
979
|
-
--- get_reverse_best_neighbors_by_gene(genes_id,
|
1157
|
+
--- get_reverse_best_neighbors_by_gene(string:genes_id, int:offset, int:limit)
|
980
1158
|
|
981
1159
|
�������å�¦����ʪ�狼�鸫�ƥ����꤬�٥��ȥҥåȤȤʤ�����Ҥ����ޤ���
|
982
1160
|
|
@@ -988,7 +1166,7 @@ SSDB
|
|
988
1166
|
get_reverse_best_neighbors_by_gene('eco:b0002', 1, 10)
|
989
1167
|
get_reverse_best_neighbors_by_gene('eco:b0002', 11, 10)
|
990
1168
|
|
991
|
-
--- get_paralogs_by_gene(genes_id,
|
1169
|
+
--- get_paralogs_by_gene(string:genes_id, int:offset, int:limit)
|
992
1170
|
|
993
1171
|
�������Ʊ����ʪ����ǥѥ���������Ҥ����ޤ���
|
994
1172
|
|
@@ -1000,21 +1178,10 @@ SSDB
|
|
1000
1178
|
get_paralogs_by_gene('eco:b0002', 1, 10)
|
1001
1179
|
get_paralogs_by_gene('eco:b0002', 11, 10)
|
1002
1180
|
|
1003
|
-
#--- get_similarity_between_genes(genes_id1, genes_id2)
|
1004
|
-
#
|
1005
|
-
#���ꤷ�����Ĥΰ����Ҵ֤� Smith-Waterman ��������ޤ�ǡ������֤��ޤ���
|
1006
|
-
#
|
1007
|
-
#���͡�
|
1008
|
-
# SSDBRelation
|
1009
|
-
#
|
1010
|
-
#�㡧
|
1011
|
-
# # ��IJ�ݤ� b0002 �����Ҥ� b3940 �����Ҵ֤Υ������䥢�饤�����ΰ������
|
1012
|
-
# get_similarity_between_genes('eco:b0002', 'eco:b3940')
|
1013
|
-
|
1014
1181
|
|
1015
1182
|
==== Motif
|
1016
1183
|
|
1017
|
-
--- get_motifs_by_gene(genes_id, db)
|
1184
|
+
--- get_motifs_by_gene(string:genes_id, string:db)
|
1018
1185
|
|
1019
1186
|
���ꤷ�������Ҥ�¸�ߤ��������դΥꥹ�Ȥ��֤��ޤ���������եǡ����١���
|
1020
1187
|
�Υꥹ�Ȥˤϡ�Pfam (pfam), TIGRFAM (tfam), PROSITE pattern (pspt), PROSITE
|
@@ -1027,7 +1194,7 @@ profile (pspf)
|
|
1027
1194
|
# ��IJ�ݤΰ����� b0002 ����Pfam������դΥꥹ��
|
1028
1195
|
get_motifs_by_gene('eco:b0002', 'pfam')
|
1029
1196
|
|
1030
|
-
--- get_genes_by_motifs(motif_id_list,
|
1197
|
+
--- get_genes_by_motifs([string]:motif_id_list, int:offset, int:limit)
|
1031
1198
|
|
1032
1199
|
���ꤷ��������դ����ƻ��İ����Ҥ����ޤ���
|
1033
1200
|
|
@@ -1040,14 +1207,13 @@ profile (pspf)
|
|
1040
1207
|
get_genes_by_motifs(list, 1, 10)
|
1041
1208
|
get_genes_by_motifs(list, 11, 10)
|
1042
1209
|
|
1043
|
-
|
1044
|
-
==== KO, OC, PC
|
1210
|
+
==== KO
|
1045
1211
|
|
1046
1212
|
KO (KEGG orthology), OC (KEGG ortholog cluster), PC (KEGG paralog cluster) ��
|
1047
1213
|
��������뤿��Υ�åɤǤ���KO �ϥ���졼����줿���������������ҷ���
|
1048
1214
|
OC �� PC �ϵ���Ū�˥��饹������줿��Ʊ���Τ�������ҷ��Υǡ����١����Ǥ���
|
1049
1215
|
|
1050
|
-
--- get_ko_by_gene(genes_id)
|
1216
|
+
--- get_ko_by_gene(string:genes_id)
|
1051
1217
|
|
1052
1218
|
���ꤷ�������Ҥ˥�������Ƥ��� KO �Υ���ȥ��ֹ�������֤��ޤ���
|
1053
1219
|
|
@@ -1058,18 +1224,8 @@ OC
|
|
1058
1224
|
# eco:b0002 �����Ҥ˥�������Ƥ��� KO �Υꥹ��
|
1059
1225
|
get_ko_by_gene('eco:b0002')
|
1060
1226
|
|
1061
|
-
#--- get_ko_members(ko_id)
|
1062
|
-
#
|
1063
|
-
#���ꤷ�� ko_id �� KO ����ȥ�˴ޤޤ������ҤΥꥹ�Ȥ��֤��ޤ���
|
1064
|
-
#
|
1065
|
-
#���͡�
|
1066
|
-
# ArrayOfstring (genes_id)
|
1067
|
-
#
|
1068
|
-
#�㡧
|
1069
|
-
# # KO �ֹ� K02208 �Υ�������Ƥ�������ҤΥꥹ��
|
1070
|
-
# get_ko_by_gene('ko:K02598')
|
1071
1227
|
|
1072
|
-
--- get_ko_by_ko_class(ko_class_id)
|
1228
|
+
--- get_ko_by_ko_class(string:ko_class_id)
|
1073
1229
|
|
1074
1230
|
���ꤷ�� ko_class_id �˴ޤޤ�� ko_id �Υꥹ�Ȥ��֤��ޤ���
|
1075
1231
|
|
@@ -1080,7 +1236,7 @@ OC
|
|
1080
1236
|
# KO class '01196' �˴ޤޤ�� KO �Υꥹ��
|
1081
1237
|
get_ko_by_ko_class('01196')
|
1082
1238
|
|
1083
|
-
--- get_genes_by_ko_class(ko_class_id, org,
|
1239
|
+
--- get_genes_by_ko_class(string:ko_class_id, string:org, int:offset, int:limit)
|
1084
1240
|
|
1085
1241
|
���ꤷ����ʪ��� ko_class_id �˴ޤޤ������ҤΥꥹ�Ȥ��֤��ޤ���
|
1086
1242
|
|
@@ -1091,7 +1247,7 @@ OC
|
|
1091
1247
|
# KO ���饹 '00930' �˴ޤޤ��ҥȰ����ҤΥꥹ��
|
1092
1248
|
get_genes_by_ko_class('00903', 'hsa' , 1, 100)
|
1093
1249
|
|
1094
|
-
--- get_genes_by_ko(ko_id, org)
|
1250
|
+
--- get_genes_by_ko(string:ko_id, string:org)
|
1095
1251
|
|
1096
1252
|
���ꤷ����ʪ��� ko_id �˴ޤޤ������ҤΥꥹ�Ȥ��֤��ޤ���
|
1097
1253
|
��ʪ�拾���ɤ� all ����ꤹ�������ʪ��ΰ����Ҥ��֤��ޤ���
|
@@ -1106,29 +1262,6 @@ OC
|
|
1106
1262
|
# KO �ֹ� 'K00010' �˴ޤޤ������ʪ��ΰ����ҥꥹ��
|
1107
1263
|
get_genes_by_ko('ko:K00010', 'all')
|
1108
1264
|
|
1109
|
-
--- get_oc_members_by_gene(genes_id, start, max_results)
|
1110
|
-
|
1111
|
-
���ꤷ�������Ҥ�Ʊ�� OC ��°��������ҤΥꥹ�Ȥ��֤��ޤ���
|
1112
|
-
|
1113
|
-
���͡�
|
1114
|
-
ArrayOfstring (genes_id)
|
1115
|
-
|
1116
|
-
�㡧
|
1117
|
-
# eco:b0002 �����Ҥ�Ʊ���������������饹�����˴ޤޤ������ҤΥꥹ��
|
1118
|
-
get_oc_members_by_gene('eco:b0002', 1, 10)
|
1119
|
-
get_oc_members_by_gene('eco:b0002', 11, 10)
|
1120
|
-
|
1121
|
-
--- get_pc_members_by_gene(genes_id, start, max_results)
|
1122
|
-
|
1123
|
-
���ꤷ�������Ҥ�Ʊ�� PC ��°��������ҤΥꥹ�Ȥ��֤��ޤ���
|
1124
|
-
|
1125
|
-
���͡�
|
1126
|
-
ArrayOfstring (genes_id)
|
1127
|
-
|
1128
|
-
�㡧
|
1129
|
-
# eco:b0002 �����Ҥ�Ʊ���ѥ�������饹�����˴ޤޤ������ҤΥꥹ��
|
1130
|
-
get_pc_members_by_gene('eco:b0002', 1, 10)
|
1131
|
-
get_pc_members_by_gene('eco:b0002', 11, 10)
|
1132
1265
|
|
1133
1266
|
|
1134
1267
|
==== PATHWAY
|
@@ -1140,7 +1273,10 @@ PATHWAY
|
|
1140
1273
|
|
1141
1274
|
+ �ѥ��������ؤο��Ť�
|
1142
1275
|
|
1143
|
-
|
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)
|
1144
1280
|
|
1145
1281
|
���ꤷ����ʪ��ǡ�Ϳ����줿�ѥ��������ޥåפ�Ϳ����줿���֥�������
|
1146
1282
|
�ʰ����ҡ�����ʪ�������ֹ�ˤ��б������Ȥ˿���Ĥ���������������
|
@@ -1155,7 +1291,7 @@ PATHWAY
|
|
1155
1291
|
obj_list = ['eco:b0002', 'cpd:C00263']
|
1156
1292
|
mark_pathway_by_objects('path:eco00260', obj_list)
|
1157
1293
|
|
1158
|
-
--- color_pathway_by_objects(pathway_id, object_id_list, fg_color_list, bg_color_list)
|
1294
|
+
--- color_pathway_by_objects(string:pathway_id, [string]:object_id_list, [string]:fg_color_list, [string]:bg_color_list)
|
1159
1295
|
|
1160
1296
|
���ꤷ���ѥ���������Ϳ����줿���֥������ȡʰ����ҡ�����ʪ�����ǡˤ��Ф���
|
1161
1297
|
ʸ�����Ȥ� fg_color_list �ǻ��ꤷ�������طʤ� bg_color_list �ǻ��ꤷ������
|
@@ -1174,7 +1310,7 @@ bg_color_list
|
|
1174
1310
|
bg_list = ['#ff0000', 'yellow']
|
1175
1311
|
color_pathway_by_objects('path:eco00053', obj_list, fg_list, bg_list)
|
1176
1312
|
|
1177
|
-
--- color_pathway_by_elements(pathway_id, element_id_list, fg_color_list, bg_color_list)
|
1313
|
+
--- color_pathway_by_elements(string:pathway_id, [int]:element_id_list, [string]:fg_color_list, [string]:bg_color_list)
|
1178
1314
|
|
1179
1315
|
���ꤷ�� element_id ���б�����ѥ���������Υ��֥������ȡ�Ĺ������ݤʤɡ�
|
1180
1316
|
���Ф���ʸ�����Ȥ� fg_color_list �ǻ��ꤷ�������طʤ� bg_color_list ��
|
@@ -1213,7 +1349,7 @@ KGML
|
|
1213
1349
|
bg_list = [ '#ffff00', '#ffff00', '#ffcc00', '#ffcc00' ]
|
1214
1350
|
color_pathway_by_elements('path:bsu00010', element_id_list, fg_list, bg_list)
|
1215
1351
|
|
1216
|
-
--- get_html_of_marked_pathway_by_objects(pathway_id, object_id_list)
|
1352
|
+
--- get_html_of_marked_pathway_by_objects(string:pathway_id, [string]:object_id_list)
|
1217
1353
|
|
1218
1354
|
����������˥���å��֥�ޥåפ�ޤ� HTML �ڡ����� URL ���֤�
|
1219
1355
|
�С������� 'mark_pathway_by_objects' ��åɤǤ���
|
@@ -1228,7 +1364,7 @@ KGML
|
|
1228
1364
|
obj_list = ['eco:b4258', 'cpd:C00135', 'ko:K01881']
|
1229
1365
|
get_html_of_marked_pathway_by_objects('path:eco00970', obj_list)
|
1230
1366
|
|
1231
|
-
--- get_html_of_colored_pathway_by_objects(pathway_id, object_id_list, fg_color_list, bg_color_list)
|
1367
|
+
--- get_html_of_colored_pathway_by_objects(string:pathway_id, [string]:object_id_list, [string]:fg_color_list, [string]:bg_color_list)
|
1232
1368
|
|
1233
1369
|
����������˥���å��֥�ޥåפ�ޤ� HTML �ڡ����� URL ���֤�
|
1234
1370
|
�С������� 'color_pathway_by_objects' ��åɤǤ���
|
@@ -1245,7 +1381,7 @@ KGML
|
|
1245
1381
|
bg_list = ['#ff0000', 'yellow', 'orange']
|
1246
1382
|
get_html_of_colored_pathway_by_objects('path:eco00970', obj_list, fg_list, bg_list)
|
1247
1383
|
|
1248
|
-
--- get_html_of_colored_pathway_by_elements(pathway_id, element_id_list, fg_color_list, bg_color_list)
|
1384
|
+
--- get_html_of_colored_pathway_by_elements(string:pathway_id, [int]:element_id_list, [string]:fg_color_list, [string]:bg_color_list)
|
1249
1385
|
|
1250
1386
|
����������˥���å��֥�ޥåפ�ޤ� HTML �ڡ����� URL ���֤�
|
1251
1387
|
�С������� 'color_pathway_by_elements' ��åɤǤ���
|
@@ -1265,9 +1401,38 @@ KGML
|
|
1265
1401
|
bg_list = [ '#ffff00', '#ffff00', '#ffcc00', '#ffcc00' ]
|
1266
1402
|
color_pathway_by_elements('path:bsu00010', element_id_list, fg_list, bg_list)
|
1267
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
|
+
|
1268
1433
|
+ �ѥ���������Υ��֥������ȸ���
|
1269
1434
|
|
1270
|
-
--- get_elements_by_pathway(pathway_id)
|
1435
|
+
--- get_elements_by_pathway(string:pathway_id)
|
1271
1436
|
|
1272
1437
|
���ꤷ���ѥ���������˺ܤäƤ��륪�֥����������ǤΥꥹ�Ȥ��֤��ޤ���
|
1273
1438
|
����ˡ�ˤĤ��Ƥ� color_pathway_by_elements ��åɤȤ��Ƥ���������
|
@@ -1292,7 +1457,7 @@ KGML
|
|
1292
1457
|
end
|
1293
1458
|
end
|
1294
1459
|
|
1295
|
-
--- get_genes_by_pathway(pathway_id)
|
1460
|
+
--- get_genes_by_pathway(string:pathway_id)
|
1296
1461
|
|
1297
1462
|
���ꤷ���ѥ���������˺ܤäƤ�������ҤΥꥹ�Ȥ��֤��ޤ�����ʪ��̾��
|
1298
1463
|
pathway_id �˴ޤޤ�� keggorg �ǻ��ꤷ�ޤ���
|
@@ -1304,7 +1469,7 @@ pathway_id
|
|
1304
1469
|
# ��IJ�ݤΥѥ������� 00020 �֤˺ܤäƤ�������ҤΥꥹ��
|
1305
1470
|
get_genes_by_pathway('path:eco00020')
|
1306
1471
|
|
1307
|
-
--- get_enzymes_by_pathway(pathway_id)
|
1472
|
+
--- get_enzymes_by_pathway(string:pathway_id)
|
1308
1473
|
|
1309
1474
|
���ꤷ���ѥ��������˺ܤäƤ�������ֹ�Υꥹ�Ȥ��֤��ޤ���
|
1310
1475
|
|
@@ -1315,7 +1480,7 @@ pathway_id
|
|
1315
1480
|
# ��IJ�ݤΥѥ������� 00020 �֤˺ܤäƤ�������ֹ�Υꥹ��
|
1316
1481
|
get_enzymes_by_pathway('path:eco00020')
|
1317
1482
|
|
1318
|
-
--- get_compounds_by_pathway(pathway_id)
|
1483
|
+
--- get_compounds_by_pathway(string:pathway_id)
|
1319
1484
|
|
1320
1485
|
���ꤷ���ѥ��������˺ܤäƤ��벽��ʪ�Υꥹ�Ȥ��֤��ޤ���
|
1321
1486
|
|
@@ -1326,7 +1491,7 @@ pathway_id
|
|
1326
1491
|
# ��IJ�ݤΥѥ������� 00020 �˺ܤäƤ��벽��ʪ�Υꥹ��
|
1327
1492
|
get_compounds_by_pathway('path:eco00020')
|
1328
1493
|
|
1329
|
-
--- get_glycans_by_pathway(pathway_id)
|
1494
|
+
--- get_glycans_by_pathway(string:pathway_id)
|
1330
1495
|
|
1331
1496
|
���ꤷ���ѥ��������˺ܤäƤ��������Υꥹ�Ȥ��֤��ޤ���
|
1332
1497
|
|
@@ -1337,7 +1502,7 @@ pathway_id
|
|
1337
1502
|
# ��IJ�ݤΥѥ������� 00510 �˺ܤäƤ��������Υꥹ��
|
1338
1503
|
get_glycans_by_pathway('path:eco00510')
|
1339
1504
|
|
1340
|
-
--- get_reactions_by_pathway(pathway_id)
|
1505
|
+
--- get_reactions_by_pathway(string:pathway_id)
|
1341
1506
|
|
1342
1507
|
���ꤷ���ѥ��������˺ܤäƤ���ꥢ��������ֹ�Υꥹ�Ȥ��֤��ޤ���
|
1343
1508
|
|
@@ -1348,7 +1513,7 @@ pathway_id
|
|
1348
1513
|
# ��IJ�ݤΥѥ������� 00260 �֤˺ܤäƤ���ꥢ�������Υꥹ��
|
1349
1514
|
get_reactions_by_pathway('path:eco00260')
|
1350
1515
|
|
1351
|
-
--- get_kos_by_pathway(pathway_id)
|
1516
|
+
--- get_kos_by_pathway(string:pathway_id)
|
1352
1517
|
|
1353
1518
|
���ꤷ���ѥ��������˺ܤäƤ��� KO �ֹ�Υꥹ�Ȥ��֤��ޤ���
|
1354
1519
|
|
@@ -1359,11 +1524,12 @@ pathway_id
|
|
1359
1524
|
# �ҥȤΥѥ������� 00010 �˺ܤäƤ��� KO �ֹ�Υꥹ��
|
1360
1525
|
get_kos_by_pathway('path:hsa00010')
|
1361
1526
|
|
1362
|
-
|
1363
|
-
|
1364
1527
|
+ ���֥������Ȥ���ѥ�����������
|
1365
1528
|
|
1366
|
-
|
1529
|
+
��Ϣ URL��
|
1530
|
+
* ((<URL:http://www.genome.jp/kegg/tool/search_pathway.html>))
|
1531
|
+
|
1532
|
+
--- get_pathways_by_genes([string]:genes_id_list)
|
1367
1533
|
|
1368
1534
|
���ꤷ�������Ҥ����ƺܤäƤ���ѥ��������Υꥹ�Ȥ��֤��ޤ���
|
1369
1535
|
|
@@ -1374,7 +1540,7 @@ pathway_id
|
|
1374
1540
|
# ��IJ�ݤΰ����� b0077 �� b0078 ��ξ���ܤäƤ���ѥ��������Υꥹ��
|
1375
1541
|
get_pathways_by_genes(['eco:b0077', 'eco:b0078'])
|
1376
1542
|
|
1377
|
-
--- get_pathways_by_enzymes(enzyme_id_list)
|
1543
|
+
--- get_pathways_by_enzymes([string]:enzyme_id_list)
|
1378
1544
|
|
1379
1545
|
���ꤷ�������ֹ椬���ƺܤäƤ���ѥ��������Υꥹ�Ȥ��֤��ޤ���
|
1380
1546
|
|
@@ -1385,7 +1551,7 @@ pathway_id
|
|
1385
1551
|
# �����ֹ� 1.3.99.1 �ι��Ǥ��ܤäƤ���ѥ��������Υꥹ��
|
1386
1552
|
get_pathways_by_enzymes(['ec:1.3.99.1'])
|
1387
1553
|
|
1388
|
-
--- get_pathways_by_compounds(compound_id_list)
|
1554
|
+
--- get_pathways_by_compounds([string]:compound_id_list)
|
1389
1555
|
|
1390
1556
|
���ꤷ������ʪ�����ƺܤäƤ���ѥ��������Υꥹ�Ȥ��֤��ޤ���
|
1391
1557
|
|
@@ -1396,7 +1562,7 @@ pathway_id
|
|
1396
1562
|
# ����ʪ C00033 �� C00158 ��ξ���ܤäƤ���ѥ��������Υꥹ��
|
1397
1563
|
get_pathways_by_compounds(['cpd:C00033', 'cpd:C00158'])
|
1398
1564
|
|
1399
|
-
--- get_pathways_by_glycans(compound_id_list)
|
1565
|
+
--- get_pathways_by_glycans([string]:compound_id_list)
|
1400
1566
|
|
1401
1567
|
���ꤷ�����������ƺܤäƤ���ѥ��������Υꥹ�Ȥ��֤��ޤ���
|
1402
1568
|
|
@@ -1407,7 +1573,7 @@ pathway_id
|
|
1407
1573
|
# ���� G00009 �� G00011 ��ξ���ܤäƤ���ѥ��������Υꥹ��
|
1408
1574
|
get_pathways_by_glycans(['gl:G00009', 'gl:G00011'])
|
1409
1575
|
|
1410
|
-
--- get_pathways_by_reactions(reaction_id_list)
|
1576
|
+
--- get_pathways_by_reactions([string]:reaction_id_list)
|
1411
1577
|
|
1412
1578
|
���ꤷ���ꥢ��������ֹ椬���ƺܤäƤ���ѥ��������Υꥹ�Ȥ��֤��ޤ���
|
1413
1579
|
|
@@ -1419,7 +1585,7 @@ pathway_id
|
|
1419
1585
|
# ȿ����ޤ�ѥ��������Υꥹ��
|
1420
1586
|
get_pathways_by_reactions(['rn:R00959', 'rn:R02740', 'rn:R00960', 'rn:R01786'])
|
1421
1587
|
|
1422
|
-
--- get_pathways_by_kos(ko_id_list, org)
|
1588
|
+
--- get_pathways_by_kos([string]:ko_id_list, string:org)
|
1423
1589
|
|
1424
1590
|
���ꤷ����ʪ�� KO �ֹ椬���ƺܤäƤ���ѥ��������Υꥹ�Ȥ��֤��ޤ���
|
1425
1591
|
|
@@ -1433,10 +1599,9 @@ pathway_id
|
|
1433
1599
|
# KO �ֹ� 'ko:K00016' �� 'ko:K00382' ��ޤ�����ʪ��Υѥ��������Υꥹ��
|
1434
1600
|
get_pathways_by_kos(['ko:K00016', 'ko:K00382'], 'all')
|
1435
1601
|
|
1436
|
-
|
1437
1602
|
+ �ѥ��������֤δط�
|
1438
1603
|
|
1439
|
-
--- get_linked_pathways(pathway_id)
|
1604
|
+
--- get_linked_pathways(string:pathway_id)
|
1440
1605
|
|
1441
1606
|
���ꤷ���ѥ��������ֹ�Υѥ���������������Ƥ���ѥ���������
|
1442
1607
|
�ꥹ�Ȥ��֤��ޤ���
|
@@ -1448,7 +1613,6 @@ pathway_id
|
|
1448
1613
|
# �ѥ������� path:eco00620 ��������Ƥ���ѥ��������Υꥹ��
|
1449
1614
|
get_linked_pathways('path:eco00620')
|
1450
1615
|
|
1451
|
-
|
1452
1616
|
==== GENES
|
1453
1617
|
|
1454
1618
|
GENES �ǡ����١������Ф����åɤΰ����Ǥ���GENES �ǡ����١����ˤĤ���
|
@@ -1456,9 +1620,9 @@ GENES
|
|
1456
1620
|
|
1457
1621
|
* ((<URL:http://www.genome.jp/kegg/kegg2.html#genes>))
|
1458
1622
|
|
1459
|
-
--- get_genes_by_organism(org,
|
1623
|
+
--- get_genes_by_organism(string:org, int:offset, int:limit)
|
1460
1624
|
|
1461
|
-
���ꤷ����ʪ����� GENES ����ȥ�Τ�����
|
1625
|
+
���ꤷ����ʪ����� GENES ����ȥ�Τ�����offset ���ܤ��� limit ʬ��
|
1462
1626
|
��̤��֤��ޤ���
|
1463
1627
|
|
1464
1628
|
���͡�
|
@@ -1469,7 +1633,6 @@ GENES
|
|
1469
1633
|
get_genes_by_organism('hin', 1, 100)
|
1470
1634
|
get_genes_by_organism('hin', 101, 100)
|
1471
1635
|
|
1472
|
-
|
1473
1636
|
==== GENOME
|
1474
1637
|
|
1475
1638
|
GENOME �ǡ����١������Ф����åɤΰ����Ǥ���GENOME �ǡ����١����ˤĤ���
|
@@ -1477,7 +1640,7 @@ GENOME
|
|
1477
1640
|
|
1478
1641
|
* ((<URL:http://www.genome.jp/kegg/kegg2.html#genome>))
|
1479
1642
|
|
1480
|
-
--- get_number_of_genes_by_organism(org)
|
1643
|
+
--- get_number_of_genes_by_organism(string:org)
|
1481
1644
|
|
1482
1645
|
���ꤷ����ʪ�郎���İ����ҿ����֤��ޤ���
|
1483
1646
|
|
@@ -1488,25 +1651,184 @@ GENOME
|
|
1488
1651
|
# ��IJ�ݤ����İ����Ҥο�
|
1489
1652
|
get_number_of_genes_by_organism('eco')
|
1490
1653
|
|
1491
|
-
|
1492
1654
|
==== LIGAND
|
1493
1655
|
|
1494
1656
|
LIGAND �ǡ����١������Ф����åɤΰ����Ǥ���
|
1495
1657
|
|
1496
|
-
|
1658
|
+
��Ϣ URL��
|
1659
|
+
* ((<URL:http://www.genome.jp/kegg/ligand.html>))
|
1660
|
+
|
1661
|
+
--- convert_mol_to_kcf(string:mol)
|
1497
1662
|
|
1498
1663
|
MOL �ե����ޥåȤΥ���ȥ�� KCF �ե����ޥåȤ��Ѵ����ޤ���
|
1499
1664
|
|
1500
1665
|
���͡�
|
1501
|
-
|
1666
|
+
string
|
1502
1667
|
|
1503
1668
|
�㡧
|
1504
1669
|
convert_mol_to_kcf(mol_str)
|
1505
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/>))
|
1506
1828
|
|
1507
1829
|
== Notes
|
1508
1830
|
|
1509
|
-
Last updated:
|
1831
|
+
Last updated: December 27, 2006
|
1510
1832
|
|
1511
1833
|
=end
|
1512
1834
|
|