bio 1.0.0 → 1.1.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (340) hide show
  1. data/bin/bioruby +14 -122
  2. data/bin/br_biofetch.rb +2 -2
  3. data/bin/br_bioflat.rb +2 -2
  4. data/bin/br_biogetseq.rb +2 -2
  5. data/bin/br_pmfetch.rb +3 -3
  6. data/doc/Changes-0.7.rd +77 -0
  7. data/doc/KEGG_API.rd +523 -232
  8. data/doc/KEGG_API.rd.ja +529 -207
  9. data/doc/Tutorial.rd +48 -11
  10. data/lib/bio.rb +59 -6
  11. data/lib/bio/alignment.rb +713 -103
  12. data/lib/bio/appl/bl2seq/report.rb +2 -18
  13. data/lib/bio/appl/blast.rb +108 -91
  14. data/lib/bio/appl/blast/format0.rb +33 -18
  15. data/lib/bio/appl/blast/format8.rb +6 -20
  16. data/lib/bio/appl/blast/report.rb +293 -429
  17. data/lib/bio/appl/blast/rexml.rb +8 -22
  18. data/lib/bio/appl/blast/wublast.rb +21 -12
  19. data/lib/bio/appl/blast/xmlparser.rb +180 -183
  20. data/lib/bio/appl/blat/report.rb +127 -30
  21. data/lib/bio/appl/clustalw.rb +87 -59
  22. data/lib/bio/appl/clustalw/report.rb +20 -22
  23. data/lib/bio/appl/emboss.rb +113 -20
  24. data/lib/bio/appl/fasta.rb +173 -198
  25. data/lib/bio/appl/fasta/format10.rb +244 -347
  26. data/lib/bio/appl/gcg/msf.rb +212 -0
  27. data/lib/bio/appl/gcg/seq.rb +195 -0
  28. data/lib/bio/appl/genscan/report.rb +5 -23
  29. data/lib/bio/appl/hmmer.rb +8 -45
  30. data/lib/bio/appl/hmmer/report.rb +2 -20
  31. data/lib/bio/appl/iprscan/report.rb +374 -0
  32. data/lib/bio/appl/mafft.rb +87 -50
  33. data/lib/bio/appl/mafft/report.rb +151 -44
  34. data/lib/bio/appl/muscle.rb +52 -0
  35. data/lib/bio/appl/phylip/alignment.rb +129 -0
  36. data/lib/bio/appl/phylip/distance_matrix.rb +96 -0
  37. data/lib/bio/appl/probcons.rb +41 -0
  38. data/lib/bio/appl/psort.rb +89 -96
  39. data/lib/bio/appl/psort/report.rb +6 -22
  40. data/lib/bio/appl/pts1.rb +263 -0
  41. data/lib/bio/appl/sim4.rb +26 -36
  42. data/lib/bio/appl/sim4/report.rb +2 -18
  43. data/lib/bio/appl/sosui/report.rb +5 -20
  44. data/lib/bio/appl/spidey/report.rb +2 -2
  45. data/lib/bio/appl/targetp/report.rb +4 -20
  46. data/lib/bio/appl/tcoffee.rb +55 -0
  47. data/lib/bio/appl/tmhmm/report.rb +4 -20
  48. data/lib/bio/command.rb +235 -64
  49. data/lib/bio/data/aa.rb +21 -26
  50. data/lib/bio/data/codontable.rb +2 -20
  51. data/lib/bio/data/na.rb +19 -4
  52. data/lib/bio/db.rb +27 -12
  53. data/lib/bio/db/aaindex.rb +2 -20
  54. data/lib/bio/db/embl/common.rb +4 -21
  55. data/lib/bio/db/embl/embl.rb +33 -85
  56. data/lib/bio/db/embl/sptr.rb +612 -302
  57. data/lib/bio/db/embl/swissprot.rb +10 -29
  58. data/lib/bio/db/embl/trembl.rb +10 -29
  59. data/lib/bio/db/embl/uniprot.rb +10 -29
  60. data/lib/bio/db/fantom.rb +15 -20
  61. data/lib/bio/db/fasta.rb +3 -3
  62. data/lib/bio/db/genbank/common.rb +37 -46
  63. data/lib/bio/db/genbank/ddbj.rb +6 -18
  64. data/lib/bio/db/genbank/genbank.rb +47 -186
  65. data/lib/bio/db/genbank/genpept.rb +4 -17
  66. data/lib/bio/db/genbank/refseq.rb +4 -17
  67. data/lib/bio/db/gff.rb +103 -35
  68. data/lib/bio/db/go.rb +4 -20
  69. data/lib/bio/db/kegg/brite.rb +26 -36
  70. data/lib/bio/db/kegg/compound.rb +81 -85
  71. data/lib/bio/db/kegg/drug.rb +98 -0
  72. data/lib/bio/db/kegg/enzyme.rb +133 -110
  73. data/lib/bio/db/kegg/expression.rb +2 -20
  74. data/lib/bio/db/kegg/genes.rb +208 -238
  75. data/lib/bio/db/kegg/genome.rb +164 -285
  76. data/lib/bio/db/kegg/glycan.rb +114 -157
  77. data/lib/bio/db/kegg/keggtab.rb +242 -303
  78. data/lib/bio/db/kegg/kgml.rb +117 -160
  79. data/lib/bio/db/kegg/orthology.rb +112 -0
  80. data/lib/bio/db/kegg/reaction.rb +54 -69
  81. data/lib/bio/db/kegg/taxonomy.rb +331 -0
  82. data/lib/bio/db/lasergene.rb +209 -0
  83. data/lib/bio/db/litdb.rb +3 -27
  84. data/lib/bio/db/medline.rb +228 -249
  85. data/lib/bio/db/nbrf.rb +3 -3
  86. data/lib/bio/db/newick.rb +510 -0
  87. data/lib/bio/db/nexus.rb +1854 -0
  88. data/lib/bio/db/pdb.rb +5 -17
  89. data/lib/bio/db/pdb/atom.rb +2 -18
  90. data/lib/bio/db/pdb/chain.rb +2 -18
  91. data/lib/bio/db/pdb/chemicalcomponent.rb +2 -18
  92. data/lib/bio/db/pdb/model.rb +2 -18
  93. data/lib/bio/db/pdb/pdb.rb +73 -34
  94. data/lib/bio/db/pdb/residue.rb +4 -20
  95. data/lib/bio/db/pdb/utils.rb +2 -18
  96. data/lib/bio/db/prosite.rb +403 -422
  97. data/lib/bio/db/rebase.rb +84 -40
  98. data/lib/bio/db/soft.rb +404 -0
  99. data/lib/bio/db/transfac.rb +5 -17
  100. data/lib/bio/feature.rb +106 -52
  101. data/lib/bio/io/das.rb +32 -42
  102. data/lib/bio/io/dbget.rb +2 -20
  103. data/lib/bio/io/ddbjxml.rb +77 -138
  104. data/lib/bio/io/ebisoap.rb +158 -0
  105. data/lib/bio/io/ensembl.rb +229 -0
  106. data/lib/bio/io/fastacmd.rb +89 -82
  107. data/lib/bio/io/fetch.rb +163 -96
  108. data/lib/bio/io/flatfile.rb +170 -73
  109. data/lib/bio/io/flatfile/bdb.rb +3 -16
  110. data/lib/bio/io/flatfile/index.rb +2 -2
  111. data/lib/bio/io/flatfile/indexer.rb +3 -2
  112. data/lib/bio/io/higet.rb +12 -31
  113. data/lib/bio/io/keggapi.rb +210 -269
  114. data/lib/bio/io/ncbisoap.rb +155 -0
  115. data/lib/bio/io/pubmed.rb +169 -147
  116. data/lib/bio/io/registry.rb +4 -20
  117. data/lib/bio/io/soapwsdl.rb +43 -38
  118. data/lib/bio/io/sql.rb +242 -305
  119. data/lib/bio/location.rb +407 -285
  120. data/lib/bio/map.rb +410 -0
  121. data/lib/bio/pathway.rb +558 -695
  122. data/lib/bio/reference.rb +272 -75
  123. data/lib/bio/sequence.rb +255 -13
  124. data/lib/bio/sequence/aa.rb +71 -10
  125. data/lib/bio/sequence/common.rb +187 -33
  126. data/lib/bio/sequence/compat.rb +59 -4
  127. data/lib/bio/sequence/format.rb +54 -7
  128. data/lib/bio/sequence/generic.rb +3 -3
  129. data/lib/bio/sequence/na.rb +328 -26
  130. data/lib/bio/shell.rb +11 -4
  131. data/lib/bio/shell/core.rb +221 -160
  132. data/lib/bio/shell/demo.rb +18 -15
  133. data/lib/bio/shell/interface.rb +14 -12
  134. data/lib/bio/shell/irb.rb +95 -0
  135. data/lib/bio/shell/object.rb +45 -26
  136. data/lib/bio/shell/plugin/blast.rb +42 -0
  137. data/lib/bio/shell/plugin/codon.rb +22 -14
  138. data/lib/bio/shell/plugin/das.rb +58 -0
  139. data/lib/bio/shell/plugin/emboss.rb +2 -2
  140. data/lib/bio/shell/plugin/entry.rb +22 -11
  141. data/lib/bio/shell/plugin/flatfile.rb +2 -2
  142. data/lib/bio/shell/plugin/keggapi.rb +13 -6
  143. data/lib/bio/shell/plugin/midi.rb +4 -4
  144. data/lib/bio/shell/plugin/obda.rb +2 -2
  145. data/lib/bio/shell/plugin/psort.rb +56 -0
  146. data/lib/bio/shell/plugin/seq.rb +35 -8
  147. data/lib/bio/shell/plugin/soap.rb +87 -0
  148. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/bioruby_generator.rb +29 -0
  149. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_classes.rhtml +4 -0
  150. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_log.rhtml +27 -0
  151. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_methods.rhtml +11 -0
  152. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_modules.rhtml +4 -0
  153. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_variables.rhtml +7 -0
  154. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-bg.gif +0 -0
  155. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-console.png +0 -0
  156. data/lib/bio/shell/rails/{public/images/icon.png → vendor/plugins/generators/bioruby/templates/bioruby-gem.png} +0 -0
  157. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-link.gif +0 -0
  158. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby.css +369 -0
  159. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby.rhtml +47 -0
  160. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby_controller.rb +144 -0
  161. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby_helper.rb +47 -0
  162. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/commands.rhtml +8 -0
  163. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/history.rhtml +10 -0
  164. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/index.rhtml +22 -0
  165. data/lib/bio/shell/script.rb +25 -0
  166. data/lib/bio/shell/setup.rb +109 -0
  167. data/lib/bio/shell/web.rb +70 -58
  168. data/lib/bio/tree.rb +850 -0
  169. data/lib/bio/util/color_scheme.rb +84 -107
  170. data/lib/bio/util/color_scheme/buried.rb +5 -24
  171. data/lib/bio/util/color_scheme/helix.rb +5 -24
  172. data/lib/bio/util/color_scheme/hydropathy.rb +5 -24
  173. data/lib/bio/util/color_scheme/nucleotide.rb +5 -24
  174. data/lib/bio/util/color_scheme/strand.rb +5 -24
  175. data/lib/bio/util/color_scheme/taylor.rb +5 -24
  176. data/lib/bio/util/color_scheme/turn.rb +5 -24
  177. data/lib/bio/util/color_scheme/zappo.rb +5 -24
  178. data/lib/bio/util/contingency_table.rb +70 -43
  179. data/lib/bio/util/restriction_enzyme.rb +228 -0
  180. data/lib/bio/util/restriction_enzyme/analysis.rb +249 -0
  181. data/lib/bio/util/restriction_enzyme/analysis_basic.rb +217 -0
  182. data/lib/bio/util/restriction_enzyme/cut_symbol.rb +107 -0
  183. data/lib/bio/util/restriction_enzyme/double_stranded.rb +321 -0
  184. data/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb +130 -0
  185. data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb +103 -0
  186. data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb +38 -0
  187. data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb +76 -0
  188. data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb +107 -0
  189. data/lib/bio/util/restriction_enzyme/enzymes.yaml +7061 -0
  190. data/lib/bio/util/restriction_enzyme/range/cut_range.rb +24 -0
  191. data/lib/bio/util/restriction_enzyme/range/cut_ranges.rb +47 -0
  192. data/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb +67 -0
  193. data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +257 -0
  194. data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +242 -0
  195. data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +51 -0
  196. data/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb +41 -0
  197. data/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb +77 -0
  198. data/lib/bio/util/restriction_enzyme/single_strand.rb +199 -0
  199. data/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb +135 -0
  200. data/lib/bio/util/restriction_enzyme/single_strand_complement.rb +23 -0
  201. data/lib/bio/util/restriction_enzyme/string_formatting.rb +111 -0
  202. data/lib/bio/util/sirna.rb +4 -22
  203. data/sample/color_scheme_na.rb +4 -12
  204. data/sample/enzymes.rb +78 -0
  205. data/sample/goslim.rb +5 -13
  206. data/sample/psortplot_html.rb +4 -12
  207. data/test/data/blast/2.2.15.blastp.m7 +876 -0
  208. data/test/data/embl/AB090716.embl.rel89 +63 -0
  209. data/test/data/fasta/example1.txt +75 -0
  210. data/test/data/fasta/example2.txt +21 -0
  211. data/test/data/iprscan/merged.raw +32 -0
  212. data/test/data/iprscan/merged.txt +74 -0
  213. data/test/data/soft/GDS100_partial.soft +92 -0
  214. data/test/data/soft/GSE3457_family_partial.soft +874 -0
  215. data/test/functional/bio/io/test_ensembl.rb +103 -0
  216. data/test/functional/bio/io/test_soapwsdl.rb +5 -17
  217. data/test/unit/bio/appl/bl2seq/test_report.rb +2 -2
  218. data/test/unit/bio/appl/blast/test_report.rb +3 -16
  219. data/test/unit/bio/appl/blast/test_xmlparser.rb +4 -16
  220. data/test/unit/bio/appl/genscan/test_report.rb +3 -16
  221. data/test/unit/bio/appl/hmmer/test_report.rb +3 -16
  222. data/test/unit/bio/appl/iprscan/test_report.rb +338 -0
  223. data/test/unit/bio/appl/mafft/test_report.rb +63 -0
  224. data/test/unit/bio/appl/sosui/test_report.rb +3 -16
  225. data/test/unit/bio/appl/targetp/test_report.rb +3 -16
  226. data/test/unit/bio/appl/test_blast.rb +3 -16
  227. data/test/unit/bio/appl/test_fasta.rb +4 -16
  228. data/test/unit/bio/appl/test_pts1.rb +140 -0
  229. data/test/unit/bio/appl/tmhmm/test_report.rb +3 -16
  230. data/test/unit/bio/data/test_aa.rb +4 -17
  231. data/test/unit/bio/data/test_codontable.rb +3 -16
  232. data/test/unit/bio/data/test_na.rb +3 -3
  233. data/test/unit/bio/db/embl/test_common.rb +3 -16
  234. data/test/unit/bio/db/embl/test_embl.rb +3 -16
  235. data/test/unit/bio/db/embl/test_embl_rel89.rb +219 -0
  236. data/test/unit/bio/db/embl/test_sptr.rb +1548 -41
  237. data/test/unit/bio/db/embl/test_uniprot.rb +3 -16
  238. data/test/unit/bio/db/kegg/test_genes.rb +3 -16
  239. data/test/unit/bio/db/pdb/test_pdb.rb +7 -24
  240. data/test/unit/bio/db/test_aaindex.rb +2 -2
  241. data/test/unit/bio/db/test_fasta.rb +3 -16
  242. data/test/unit/bio/db/test_gff.rb +3 -16
  243. data/test/unit/bio/db/test_lasergene.rb +95 -0
  244. data/test/unit/bio/db/test_newick.rb +56 -0
  245. data/test/unit/bio/db/test_nexus.rb +360 -0
  246. data/test/unit/bio/db/test_prosite.rb +5 -18
  247. data/test/unit/bio/db/test_rebase.rb +11 -25
  248. data/test/unit/bio/db/test_soft.rb +138 -0
  249. data/test/unit/bio/io/test_ddbjxml.rb +5 -17
  250. data/test/unit/bio/io/test_ensembl.rb +109 -0
  251. data/test/unit/bio/io/test_fastacmd.rb +3 -16
  252. data/test/unit/bio/io/test_flatfile.rb +237 -0
  253. data/test/unit/bio/io/test_soapwsdl.rb +4 -17
  254. data/test/unit/bio/sequence/test_aa.rb +3 -3
  255. data/test/unit/bio/sequence/test_common.rb +3 -16
  256. data/test/unit/bio/sequence/test_compat.rb +3 -16
  257. data/test/unit/bio/sequence/test_na.rb +29 -3
  258. data/test/unit/bio/shell/plugin/test_seq.rb +8 -8
  259. data/test/unit/bio/test_alignment.rb +16 -27
  260. data/test/unit/bio/test_command.rb +242 -25
  261. data/test/unit/bio/test_db.rb +3 -16
  262. data/test/unit/bio/test_feature.rb +4 -16
  263. data/test/unit/bio/test_location.rb +4 -16
  264. data/test/unit/bio/test_map.rb +230 -0
  265. data/test/unit/bio/test_pathway.rb +4 -16
  266. data/test/unit/bio/test_reference.rb +2 -2
  267. data/test/unit/bio/test_sequence.rb +7 -19
  268. data/test/unit/bio/test_shell.rb +3 -16
  269. data/test/unit/bio/test_tree.rb +593 -0
  270. data/test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb +299 -0
  271. data/test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb +103 -0
  272. data/test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb +240 -0
  273. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb +100 -0
  274. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb +75 -0
  275. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb +73 -0
  276. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb +53 -0
  277. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb +104 -0
  278. data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb +83 -0
  279. data/test/unit/bio/util/restriction_enzyme/test_analysis.rb +246 -0
  280. data/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb +44 -0
  281. data/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb +115 -0
  282. data/test/unit/bio/util/restriction_enzyme/test_single_strand.rb +147 -0
  283. data/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb +147 -0
  284. data/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb +60 -0
  285. data/test/unit/bio/util/test_color_scheme.rb +6 -18
  286. data/test/unit/bio/util/test_contingency_table.rb +6 -18
  287. data/test/unit/bio/util/test_restriction_enzyme.rb +42 -0
  288. data/test/unit/bio/util/test_sirna.rb +3 -16
  289. metadata +228 -169
  290. data/doc/BioRuby.rd.ja +0 -225
  291. data/doc/Design.rd.ja +0 -341
  292. data/doc/TODO.rd.ja +0 -138
  293. data/lib/bio/appl/fasta/format6.rb +0 -37
  294. data/lib/bio/db/kegg/cell.rb +0 -88
  295. data/lib/bio/db/kegg/ko.rb +0 -178
  296. data/lib/bio/shell/rails/Rakefile +0 -10
  297. data/lib/bio/shell/rails/app/controllers/application.rb +0 -4
  298. data/lib/bio/shell/rails/app/controllers/shell_controller.rb +0 -94
  299. data/lib/bio/shell/rails/app/helpers/application_helper.rb +0 -3
  300. data/lib/bio/shell/rails/app/models/shell_connection.rb +0 -30
  301. data/lib/bio/shell/rails/app/views/layouts/shell.rhtml +0 -37
  302. data/lib/bio/shell/rails/app/views/shell/history.rhtml +0 -5
  303. data/lib/bio/shell/rails/app/views/shell/index.rhtml +0 -2
  304. data/lib/bio/shell/rails/app/views/shell/show.rhtml +0 -13
  305. data/lib/bio/shell/rails/config/boot.rb +0 -19
  306. data/lib/bio/shell/rails/config/database.yml +0 -85
  307. data/lib/bio/shell/rails/config/environment.rb +0 -53
  308. data/lib/bio/shell/rails/config/environments/development.rb +0 -19
  309. data/lib/bio/shell/rails/config/environments/production.rb +0 -19
  310. data/lib/bio/shell/rails/config/environments/test.rb +0 -19
  311. data/lib/bio/shell/rails/config/routes.rb +0 -19
  312. data/lib/bio/shell/rails/doc/README_FOR_APP +0 -2
  313. data/lib/bio/shell/rails/public/404.html +0 -8
  314. data/lib/bio/shell/rails/public/500.html +0 -8
  315. data/lib/bio/shell/rails/public/dispatch.cgi +0 -10
  316. data/lib/bio/shell/rails/public/dispatch.fcgi +0 -24
  317. data/lib/bio/shell/rails/public/dispatch.rb +0 -10
  318. data/lib/bio/shell/rails/public/favicon.ico +0 -0
  319. data/lib/bio/shell/rails/public/images/rails.png +0 -0
  320. data/lib/bio/shell/rails/public/index.html +0 -277
  321. data/lib/bio/shell/rails/public/javascripts/controls.js +0 -750
  322. data/lib/bio/shell/rails/public/javascripts/dragdrop.js +0 -584
  323. data/lib/bio/shell/rails/public/javascripts/effects.js +0 -854
  324. data/lib/bio/shell/rails/public/javascripts/prototype.js +0 -1785
  325. data/lib/bio/shell/rails/public/robots.txt +0 -1
  326. data/lib/bio/shell/rails/public/stylesheets/main.css +0 -187
  327. data/lib/bio/shell/rails/script/about +0 -3
  328. data/lib/bio/shell/rails/script/breakpointer +0 -3
  329. data/lib/bio/shell/rails/script/console +0 -3
  330. data/lib/bio/shell/rails/script/destroy +0 -3
  331. data/lib/bio/shell/rails/script/generate +0 -3
  332. data/lib/bio/shell/rails/script/performance/benchmarker +0 -3
  333. data/lib/bio/shell/rails/script/performance/profiler +0 -3
  334. data/lib/bio/shell/rails/script/plugin +0 -3
  335. data/lib/bio/shell/rails/script/process/reaper +0 -3
  336. data/lib/bio/shell/rails/script/process/spawner +0 -3
  337. data/lib/bio/shell/rails/script/process/spinner +0 -3
  338. data/lib/bio/shell/rails/script/runner +0 -3
  339. data/lib/bio/shell/rails/script/server +0 -42
  340. data/lib/bio/shell/rails/test/test_helper.rb +0 -28
@@ -1,6 +1,6 @@
1
1
  =begin
2
2
 
3
- $Id: KEGG_API.rd.ja,v 1.8 2006/02/23 04:51:23 k Exp $
3
+ $Id: KEGG_API.rd.ja,v 1.11 2006/12/27 13:40:45 k Exp $
4
4
 
5
5
  Copyright (C) 2003-2006 Toshiaki Katayama <k@bioruby.org>
6
6
 
@@ -19,6 +19,7 @@ KEGG API
19
19
  * ((<KEGG API �λȤ���>))
20
20
  * ((<Ruby �ξ��>))
21
21
  * ((<Perl �ξ��>))
22
+ * ((<Perl ��������>))
22
23
  * ((<Python �ξ��>))
23
24
  * ((<Java �ξ��>))
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
38
  * ((<�᥿����>))
35
- * ((<list_databases>)),
36
- ((<list_organisms>)),
37
- ((<list_pathways>))
39
+ * ((<list_databases>))
40
+ * ((<list_organisms>))
41
+ * ((<list_pathways>))
38
42
  * ((<DBGET>))
39
- * ((<binfo>)),
40
- ((<bfind>)),
41
- ((<bget>)),
42
- ((<btit>)),
43
- ((<bconv>))
43
+ * ((<binfo>))
44
+ * ((<bfind>))
45
+ * ((<bget>))
46
+ * ((<btit>))
47
+ * ((<bconv>))
44
48
  * ((<LinkDB>))
45
- * ((<get_linkdb_by_entry>))
46
- * ((<get_genes_by_enzyme>)),
47
- ((<get_enzymes_by_gene>))
48
- * ((<get_enzymes_by_compound>)),
49
- ((<get_enzymes_by_glycan>)),
50
- ((<get_enzymes_by_reaction>)),
51
- ((<get_compounds_by_enzyme>)),
52
- ((<get_compounds_by_reaction>)),
53
- ((<get_glycans_by_enzyme>)),
54
- ((<get_glycans_by_reaction>)),
55
- ((<get_reactions_by_enzyme>)),
56
- ((<get_reactions_by_compound>)),
57
- ((<get_reactions_by_glycan>))
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>))
58
66
  * ((<SSDB>))
59
- * ((<get_best_best_neighbors_by_gene>)),
60
- ((<get_best_neighbors_by_gene>)),
61
- ((<get_reverse_best_neighbors_by_gene>)),
62
- ((<get_paralogs_by_gene>))
63
- # * ((<get_neighbors_by_gene>)),
64
- # ((<get_similarity_between_genes>))
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>))
65
71
  * ((<Motif>))
66
- * ((<get_motifs_by_gene>)),
67
- ((<get_genes_by_motifs>))
68
- * ((<KO, OC, PC>))
69
- * ((<get_ko_by_gene>)),
70
- ((<get_ko_by_ko_class>)),
71
- ((<get_genes_by_ko_class>)),
72
- ((<get_genes_by_ko>)),
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
- * ((<mark_pathway_by_objects>)),
78
- ((<color_pathway_by_objects>)),
79
- ((<color_pathway_by_elements>)),
80
- ((<get_html_of_marked_pathway_by_objects>)),
81
- ((<get_html_of_colored_pathway_by_objects>)),
82
- ((<get_html_of_colored_pathway_by_elements>))
83
- * ((<get_elements_by_pathway>)),
84
- ((<get_genes_by_pathway>)),
85
- ((<get_enzymes_by_pathway>)),
86
- ((<get_compounds_by_pathway>)),
87
- ((<get_glycans_by_pathway>)),
88
- ((<get_reactions_by_pathway>)),
89
- ((<get_kos_by_pathway>))
90
- * ((<get_pathways_by_genes>)),
91
- ((<get_pathways_by_enzymes>)),
92
- ((<get_pathways_by_compounds>)),
93
- ((<get_pathways_by_glycans>)),
94
- ((<get_pathways_by_reactions>)),
95
- ((<get_pathways_by_kos>))
96
- * ((<get_linked_pathways>))
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).create_driver
186
+ serv = SOAP::WSDLDriverFactory.new(wsdl).create_rpc_driver
166
187
  serv.generate_explicit_type = true # SOAP �� Ruby �η��Ѵ���ͭ���ˤ���
167
188
 
168
- start = 1
169
- max_results = 5
189
+ offset = 1
190
+ limit = 5
170
191
 
171
- top5 = serv.get_best_neighbors_by_gene('eco:b0002', start, max_results)
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).create_driver
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� start, max_results ������Ƴ�����졢���٤�
197
- �������̤ο������¤����褦�ˤʤ�ޤ��������Τ��ᡢ�����Υ᥽��
198
- �ɤ����Ƥη�̤����뤿��ˤϥ롼�פ��Ѥ���ɬ�פ�����ޤ���
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).create_driver
228
+ serv = SOAP::WSDLDriverFactory.new(wsdl).create_rpc_driver
206
229
  serv.generate_explicit_type = true
207
230
 
208
- start = 1
209
- max_results = 100
231
+ offset = 1
232
+ limit = 100
210
233
 
211
234
  loop do
212
- results = serv.get_best_neighbors_by_gene('eco:b0002', start, max_results)
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
- start += max_results
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
- $start = 1;
318
- $max_results = 5;
341
+ $offset = 1;
342
+ $limit = 5;
319
343
 
320
- $top5 = $serv->get_best_neighbors_by_gene('eco:b0002', $start, $max_results);
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 �ξ��
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 �ξ��
390
481
 
391
482
  Java �Ǥ� Apache Axis �饤�֥��� axis-1.2alpha ��꿷�����С������
@@ -485,7 +576,6 @@ tcsh
485
576
 
486
577
  * ((<URL:http://www.genome.jp/kegg/soap/doc/keggapi_javadoc_ja/>))
487
578
 
488
-
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
649
  * ((<URL:http://www.genome.jp/dbget-bin/get_htext?KO>))
557
650
 
558
- * start, max_results �ϰ��٤��֤äƤ����̤ο�����ꤹ�륪�ץ����ǡ�
559
- start ���ܤ��� max_results �Ĥη�̤�������ޤ������Ƥη�̤�����ˤ�
560
- start = start + max_results �Ȥ��ƶ��������֤äƤ���ޤǷ����֤�
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
- --- list_pathways(org)
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 ���Ѵ����ޤ����б����Ƥ��볰���ǡ���
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
- --- get_linkdb_by_entry(entry_id, db, start, max_results)
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, start, max_results)
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, start, max_results)
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, start, max_results)
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, start, max_results)
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, start, max_results)
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, start, max_results)
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
- --- mark_pathway_by_objects(pathway_id, object_id_list)
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 �᥽�åɤ򻲾Ȥ��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
- --- get_pathways_by_genes(genes_id_list)
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, start, max_results)
1623
+ --- get_genes_by_organism(string:org, int:offset, int:limit)
1460
1624
 
1461
- ���ꤷ����ʪ����� GENES ����ȥ�Τ�����start ���ܤ��� max_results ʬ��
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
- --- convert_mol_to_kcf(mol_text)
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
- String
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: Feb 17, 2006
1831
+ Last updated: December 27, 2006
1510
1832
 
1511
1833
  =end
1512
1834