[BioRuby-cvs] bioruby/doc KEGG_API.rd, NONE, 1.1 KEGG_API.rd.ja, 1.6, 1.7

Wed Aug 31 09:29:03 EDT 2005

Update of /home/repository/bioruby/bioruby/doc
In directory pub.open-bio.org:/tmp/cvs-serv32284

Modified Files:
	KEGG_API.rd.ja 
Added Files:
	KEGG_API.rd 
Log Message:
* newly added English version of the KEGG API manual
* Japanese version also updated

Index: KEGG_API.rd.ja
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/KEGG_API.rd.ja,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** KEGG_API.rd.ja	24 Aug 2004 00:21:55 -0000	1.6
--- KEGG_API.rd.ja	31 Aug 2005 13:29:01 -0000	1.7
***************
*** 3,7 ****
    $Id$

!     Copyright (C) 2004 KATAYAMA Toshiaki <k at bioruby.org>

  = KEGG API
--- 3,7 ----
    $Id$

!     Copyright (C) 2003-2005 Toshiaki Katayama <k at bioruby.org>

  = KEGG API
***************
*** 43,52 ****
        * ((<get_linkdb_by_entry>))
      * ((<SSDB>))
!       * ((<get_neighbors_by_gene>)),
!         ((<get_best_best_neighbors_by_gene>)),
          ((<get_best_neighbors_by_gene>)),
          ((<get_reverse_best_neighbors_by_gene>)),
!         ((<get_paralogs_by_gene>)),
!         ((<get_similarity_between_genes>))
      * ((<Motif>))
        * ((<get_motifs_by_gene>)),
--- 43,52 ----
        * ((<get_linkdb_by_entry>))
      * ((<SSDB>))
!       * ((<get_best_best_neighbors_by_gene>)),
          ((<get_best_neighbors_by_gene>)),
          ((<get_reverse_best_neighbors_by_gene>)),
!         ((<get_paralogs_by_gene>))
! #     * ((<get_neighbors_by_gene>)),
! #       ((<get_similarity_between_genes>))
      * ((<Motif>))
        * ((<get_motifs_by_gene>)),
***************
*** 54,84 ****
      * ((<KO, OC, PC>))
        * ((<get_ko_by_gene>)),
!         ((<get_ko_members>)),
          ((<get_oc_members_by_gene>)),
          ((<get_pc_members_by_gene>))
      * ((<PATHWAY>))
        * ((<mark_pathway_by_objects>)),
!         ((<color_pathway_by_objects>))
        * ((<get_genes_by_pathway>)),
          ((<get_enzymes_by_pathway>)),
          ((<get_compounds_by_pathway>)),
!         ((<get_reactions_by_pathway>))
        * ((<get_pathways_by_genes>)),
          ((<get_pathways_by_enzymes>)),
          ((<get_pathways_by_compounds>)),
!         ((<get_pathways_by_reactions>))
        * ((<get_linked_pathways>))
        * ((<get_genes_by_enzyme>)),
          ((<get_enzymes_by_gene>))
        * ((<get_enzymes_by_compound>)),
          ((<get_enzymes_by_reaction>)),
          ((<get_compounds_by_enzyme>)),
          ((<get_compounds_by_reaction>)),
          ((<get_reactions_by_enzyme>)),
!         ((<get_reactions_by_compound>))
      * ((<GENES>))
        * ((<get_genes_by_organism>))
      * ((<GENOME>))
        * ((<get_number_of_genes_by_organism>))

  == ¥¤¥ó¥È¥í¥À¥¯¥·¥ç¥ó
--- 54,99 ----
      * ((<KO, OC, PC>))
        * ((<get_ko_by_gene>)),
!         ((<get_ko_by_ko_class>)),
!         ((<get_genes_by_ko_class>)),
!         ((<get_genes_by_ko>)),
          ((<get_oc_members_by_gene>)),
          ((<get_pc_members_by_gene>))
+ #       ((<get_ko_members>)),
      * ((<PATHWAY>))
        * ((<mark_pathway_by_objects>)),
!         ((<color_pathway_by_objects>)),
!         ((<get_html_of_marked_pathway_by_objects>)),
!         ((<get_html_of_colored_pathway_by_objects>))
        * ((<get_genes_by_pathway>)),
          ((<get_enzymes_by_pathway>)),
          ((<get_compounds_by_pathway>)),
!         ((<get_glycans_by_pathway>)),
!         ((<get_reactions_by_pathway>)),
!         ((<get_kos_by_pathway>))
        * ((<get_pathways_by_genes>)),
          ((<get_pathways_by_enzymes>)),
          ((<get_pathways_by_compounds>)),
!         ((<get_pathways_by_glycans>)),
!         ((<get_pathways_by_reactions>)),
!         ((<get_pathways_by_kos>))
        * ((<get_linked_pathways>))
        * ((<get_genes_by_enzyme>)),
          ((<get_enzymes_by_gene>))
        * ((<get_enzymes_by_compound>)),
+         ((<get_enzymes_by_glycan>)),
          ((<get_enzymes_by_reaction>)),
          ((<get_compounds_by_enzyme>)),
          ((<get_compounds_by_reaction>)),
+         ((<get_glycans_by_enzyme>)),
+         ((<get_glycans_by_reaction>)),
          ((<get_reactions_by_enzyme>)),
!         ((<get_reactions_by_compound>)),
!         ((<get_reactions_by_glycan>))
      * ((<GENES>))
        * ((<get_genes_by_organism>))
      * ((<GENOME>))
        * ((<get_number_of_genes_by_organism>))
+     * ((<LIGAND>))
+       * ((<convert_mol_to_kcf>))

  == ¥¤¥ó¥È¥í¥À¥¯¥·¥ç¥ó
***************
*** 316,320 ****
                 -> list_pathways("eco");

!   foreach $path (@{$result}) {
      print "$path->{entry_id}\t$path->{definition}\n";
    }
--- 331,335 ----
                 -> list_pathways("eco");

!   foreach $path (@{$results}) {
      print "$path->{entry_id}\t$path->{definition}\n";
    }
***************
*** 487,493 ****
    * org ¤Ï KEGG ¤Ë´Þ¤Þ¤ì¤Æ¤¤¤ëÀ¸Êª¼ï¤ò¤½¤ì¤¾¤ì£³Ê¸»ú¥³¡¼¥É¤Ç
      É½µ¤·¤¿¤â¤Î¤Ç¡¢eco ¤¬ÂçÄ²¶Ý¡¢sce ¤¬½Ð²ê¹ÚÊì¤Ê¤É¤È¤Ê¤Ã¤Æ¤¤¤Þ¤¹¡£
!     £³Ê¸»ú¥³¡¼¥É¤Î¥ê¥¹¥È¤Ï°Ê²¼¤Î¥Ú¡¼¥¸¤Ë¤¢¤ê¤Þ¤¹¡£

!     * ((<URL:http://www.genome.jp/kegg/kegg2.html#genes>))

    * db ¤Ï GenomeNet ¤ÇÄó¶¡¤µ¤ì¤Æ¤¤¤ë¥Ç¡¼¥¿¥Ù¡¼¥¹Ì¾¤Ç¤¹¡£¥Ç¡¼¥¿¥Ù¡¼¥¹Ì¾¤Î
--- 502,509 ----
    * org ¤Ï KEGG ¤Ë´Þ¤Þ¤ì¤Æ¤¤¤ëÀ¸Êª¼ï¤ò¤½¤ì¤¾¤ì£³Ê¸»ú¥³¡¼¥É¤Ç
      É½µ¤·¤¿¤â¤Î¤Ç¡¢eco ¤¬ÂçÄ²¶Ý¡¢sce ¤¬½Ð²ê¹ÚÊì¤Ê¤É¤È¤Ê¤Ã¤Æ¤¤¤Þ¤¹¡£
!     £³Ê¸»ú¥³¡¼¥É¤Î¥ê¥¹¥È¤Ï list_organisms ¥á¥½¥Ã¥É¤ä°Ê²¼¤Î¥Ú¡¼¥¸¤ò
!     »²¾È¤·¤Æ¤¯¤À¤µ¤¤¡£

!     * ((<URL:http://www.genome.jp/kegg/catalog/org_list.html>))

    * db ¤Ï GenomeNet ¤ÇÄó¶¡¤µ¤ì¤Æ¤¤¤ë¥Ç¡¼¥¿¥Ù¡¼¥¹Ì¾¤Ç¤¹¡£¥Ç¡¼¥¿¥Ù¡¼¥¹Ì¾¤Î
***************
*** 497,501 ****
      ¥æ¥Ë¡¼¥¯¤Ê ID ¤Ç¤¹¡£¤¿¤È¤¨¤Ð embl:J00231 ¤Ç EMBL ¤Î¥¨¥ó¥È¥ê J00231 ¤ò
      »Ø¤·¤Þ¤¹¡£entry_id ¤Ï¡¢°Ê²¼¤Î genes_id, enzyme_id, compound_id,
!     reaction_id, pathway_id, motif_id ¤Ê¤É¤ò´Þ¤ß¤Þ¤¹¡£

    * genes_id ¤Ï keggorg ¤È°äÅÁ»ÒÌ¾¤ò ':' ¤Ç·ë¹ç¤·¤¿ KEGG ¤Î°äÅÁ»Ò ID ¤Ç¤¹¡£
--- 513,517 ----
      ¥æ¥Ë¡¼¥¯¤Ê ID ¤Ç¤¹¡£¤¿¤È¤¨¤Ð embl:J00231 ¤Ç EMBL ¤Î¥¨¥ó¥È¥ê J00231 ¤ò
      »Ø¤·¤Þ¤¹¡£entry_id ¤Ï¡¢°Ê²¼¤Î genes_id, enzyme_id, compound_id,
!     glycan_id, reaction_id, pathway_id, motif_id ¤Ê¤É¤ò´Þ¤ß¤Þ¤¹¡£

    * genes_id ¤Ï keggorg ¤È°äÅÁ»ÒÌ¾¤ò ':' ¤Ç·ë¹ç¤·¤¿ KEGG ¤Î°äÅÁ»Ò ID ¤Ç¤¹¡£
***************
*** 508,511 ****
--- 524,530 ----
      C00158 ¤Î²½¹çÊª¤Ç¤¢¤ë¥¯¥¨¥ó»À¤ò»Ø¤·¤Þ¤¹¡£

+   * glycan_id ¤Ï gl: ¤ò¤Ä¤±¤¿²½¹çÊª¤Î ID ¤Ç¤¹¡£gl:G00050 ¤ÏÅüº¿ÈÖ¹æ
+     G00050 ¤ÎÅüº¿¤Ç¤¢¤ë Paragloboside ¤ò»Ø¤·¤Þ¤¹¡£
+ 
    * reaction_id ¤Ï REACTION ¥Ç¡¼¥¿¥Ù¡¼¥¹¤Î¥¨¥ó¥È¥êÈÖ¹æ¤Ç¡¢rn:R00959 ¤Ï
      ¥ê¥¢¥¯¥·¥ç¥óÈÖ¹æ R00959 ¤ÎÈ¿±þ (cpd:C00103 ¤È cpd:00668 ´Ö¤ÎÊÑ´¹) ¤ò
***************
*** 526,529 ****
--- 545,554 ----
      ¥°¥ë¡¼¥×¤ò»Ø¤·¤Þ¤¹¡£

+   * ko_class_id ¤Ï KO ¤ò³¬ÁØÅª¤ËÊ¬Îà¤·¤¿³Æ³¬ÁØ¡Ê¥¯¥é¥¹¡Ë¤Î ID ¤Ç¡¢
+     '01110' ¤Ï Carbohydrate Metabolism ¥¯¥é¥¹¤Ë¤Ê¤ê¤Þ¤¹¡£
+     KO ¥¯¥é¥¹¤ä KO ÈÖ¹æ¤Î¥ê¥¹¥È¤Ï°Ê²¼¤Î¥Ú¡¼¥¸¤ò»²¾È¤·¤Æ¤¯¤À¤µ¤¤¡£
+ 
+     * ((<URL:http://www.genome.jp/dbget-bin/get_htext?KO>))
+ 
    * start, max_results ¤Ï°ìÅÙ¤ËÊÖ¤Ã¤Æ¤¯¤ë·ë²Ì¤Î¿ô¤ò»ØÄê¤¹¤ë¥ª¥×¥·¥ç¥ó¤Ç¡¢
      start ÈÖÌÜ¤«¤é max_results ¸Ä¤Î·ë²Ì¤ò¼õ¤±¼è¤ê¤Þ¤¹¡£Á´¤Æ¤Î·ë²Ì¤òÆÀ¤ë¤Ë¤Ï
***************
*** 541,548 ****
  KEGG API ¤Î¥á¥½¥Ã¥É¤ÏÊ¸»úÎó¤Ê¤ÉÃ±½ã¤ÊÃÍ¤òÊÖ¤¹¤â¤Î¤À¤±¤Ç¤Ê¤¯¡¢Ê£»¨¤Ê¥Ç¡¼¥¿
  ¹½Â¤¤ò»ý¤Ã¤¿ÃÍ¤òÊÖ¤¹¾ì¹ç¤â¤¢¤ê¡¢¤½¤Î¤¿¤á¤Î¥Ç¡¼¥¿·¿¤¬ÄêµÁ¤µ¤ì¤Æ¤¤¤Þ¤¹¡£

  + SSDBRelation ·¿

! SSDB ¥Ç¡¼¥¿¥Ù¡¼¥¹¤Î³Æ¥Õ¥£¡¼¥ë¥É¤ËÂÐ±þ¤¹¤ëÃÍ¤¬Æþ¤Ã¤¿ÇÛÎó¤Ç¤¹¡£

    genes_id1         ¥¯¥¨¥ê¡¼¤Î genes_id (string)
--- 566,579 ----
  KEGG API ¤Î¥á¥½¥Ã¥É¤ÏÊ¸»úÎó¤Ê¤ÉÃ±½ã¤ÊÃÍ¤òÊÖ¤¹¤â¤Î¤À¤±¤Ç¤Ê¤¯¡¢Ê£»¨¤Ê¥Ç¡¼¥¿
  ¹½Â¤¤ò»ý¤Ã¤¿ÃÍ¤òÊÖ¤¹¾ì¹ç¤â¤¢¤ê¡¢¤½¤Î¤¿¤á¤Î¥Ç¡¼¥¿·¿¤¬ÄêµÁ¤µ¤ì¤Æ¤¤¤Þ¤¹¡£
+ API ¤Î¥á¥½¥Ã¥É¤Ë¤è¤ë¡Ê¸¡º÷¤Ê¤É¤Î¡Ë·ë²Ì¤¬¤Ê¤«¤Ã¤¿¾ì¹ç¡¢·¿¤Ë¤è¤Ã¤Æ°Ê²¼¤Î
+ Ìá¤êÃÍ¤¬ÊÖ¤µ¤ì¤Þ¤¹¡£
+   * ¶õ¤ÎÇÛÎó -- ¤â¤È¤â¤È ArrayOfOBJ ¡Ê¥ª¥Ö¥¸¥§¥¯¥È¤ÎÇÛÎó¡Ë¤òÊÖ¤¹¥á¥½¥Ã¥É¤Î¾ì¹ç
+   * ¶õ¤ÎÊ¸»úÎó -- ¤â¤È¤â¤È String ¡ÊÊ¸»úÎó¡Ë¤òÊÖ¤¹¥á¥½¥Ã¥É¤Î¾ì¹ç
+   * -1 -- ¤â¤È¤â¤È int ¡Ê¿ôÃÍ¡Ë¤òÊÖ¤¹¥á¥½¥Ã¥É¤Î¾ì¹ç
+   * NULL -- ¤â¤È¤â¤È°Ê²¼¤ÇÄêµÁ¤µ¤ì¤¿¥ª¥Ö¥¸¥§¥¯¥È¤Î¤É¤ì¤«¤òÊÖ¤¹¥á¥½¥Ã¥É¤Î¾ì¹ç

  + SSDBRelation ·¿

! SSDB ¥Ç¡¼¥¿¥Ù¡¼¥¹¤Î³Æ¥Õ¥£¡¼¥ë¥É¤ËÂÐ±þ¤¹¤ëÃÍ¤¬Æþ¤Ã¤¿¥Ç¡¼¥¿·¿¤Ç¤¹¡£

    genes_id1         ¥¯¥¨¥ê¡¼¤Î genes_id (string)
***************
*** 623,627 ****

  ÌáÃÍ¡§
!   ArrayOfDefinition

  --- list_organisms
--- 654,658 ----

  ÌáÃÍ¡§
!   ArrayOfDefinition (db, definition)

  --- list_organisms
***************
*** 630,634 ****

  ÌáÃÍ¡§
!   ArrayOfDefinition

  --- list_pathways(org)
--- 661,665 ----

  ÌáÃÍ¡§
!   ArrayOfDefinition (org, definition)

  --- list_pathways(org)
***************
*** 638,642 ****

  ÌáÃÍ¡§
!   ArrayOfDefinition

--- 669,673 ----

  ÌáÃÍ¡§
!   ArrayOfDefinition (pathway_id, definition)

***************
*** 694,698 ****
    bget("-f -n a eco:b0002 bsu:BG10065")
    # FASTA ¥Õ¥©¡¼¥Þ¥Ã¥È¤Î±ö´ðÇÛÎó¤ò¼èÆÀ
!   bget("-f -n a eco:b0002 hin:tRNA-Cys-1")

  --- btit(string)
--- 725,729 ----
    bget("-f -n a eco:b0002 bsu:BG10065")
    # FASTA ¥Õ¥©¡¼¥Þ¥Ã¥È¤Î±ö´ðÇÛÎó¤ò¼èÆÀ
!   bget("-f -n n eco:b0002 hin:tRNA-Cys-1")

  --- btit(string)
***************
*** 741,758 ****
    * ((<URL:http://www.genome.jp/kegg/ssdb/>))

! --- get_neighbors_by_gene(genes_id, org, start, max_results)
! 
! »ØÄê¤·¤¿ genes_id ¤Î°äÅÁ»Ò¤Ë¥Û¥â¥í¥¸¡¼¤Î¤¢¤ëÁ´°äÅÁ»Ò¤ò»ØÄê¤·¤¿À¸Êª¤«¤é
! ¸¡º÷¤·¤Þ¤¹¡£¤Þ¤¿ org ¤Ë 'all' ¤ò»ØÄê¤¹¤ë¤ÈÁ´À¸Êª¼ï¤«¤é¸¡º÷¤·¤Þ¤¹¡£
! 
! ÌáÃÍ¡§
!   ArrayOfSSDBRelation
! 
! Îã¡§
!   # ÂçÄ²¶Ý¤Î°äÅÁ»Ò b0002 ¤ËÁêÆ±À¤Î¤¢¤ë°äÅÁ»Ò¤òÁ´¤Æ¸¡º÷¤·¤Æ¡¢·ë²Ì¤Î£±ÈÖ
!   # ¤«¤é£±£°ÈÖÌÜ¤Þ¤Ç¤òÊÖ¤·¤Þ¤¹
!   get_neighbors_by_gene('eco:b0002', 'all' 1, 10)
!   # ¼¡¤Î£±£°¸Ä¤ò start = start + max_results ¤È¤·¤Æ¼è¤ê¤Þ¤¹
!   get_neighbors_by_gene('eco:b0002', 'all' 11, 10)

  --- get_best_best_neighbors_by_gene(genes_id, start, max_results)
--- 772,789 ----
    * ((<URL:http://www.genome.jp/kegg/ssdb/>))

! #--- get_neighbors_by_gene(genes_id, org, start, max_results)
! #
! #»ØÄê¤·¤¿ genes_id ¤Î°äÅÁ»Ò¤Ë¥Û¥â¥í¥¸¡¼¤Î¤¢¤ëÁ´°äÅÁ»Ò¤ò»ØÄê¤·¤¿À¸Êª¤«¤é
! #¸¡º÷¤·¤Þ¤¹¡£¤Þ¤¿ org ¤Ë 'all' ¤ò»ØÄê¤¹¤ë¤ÈÁ´À¸Êª¼ï¤«¤é¸¡º÷¤·¤Þ¤¹¡£
! #
! #ÌáÃÍ¡§
! #  ArrayOfSSDBRelation
! #
! #Îã¡§
! #  # ÂçÄ²¶Ý¤Î°äÅÁ»Ò b0002 ¤ËÁêÆ±À¤Î¤¢¤ë°äÅÁ»Ò¤òÁ´¤Æ¸¡º÷¤·¤Æ¡¢·ë²Ì¤Î£±ÈÖ
! #  # ¤«¤é£±£°ÈÖÌÜ¤Þ¤Ç¤òÊÖ¤·¤Þ¤¹
! #  get_neighbors_by_gene('eco:b0002', 'all' 1, 10)
! #  # ¼¡¤Î£±£°¸Ä¤ò start = start + max_results ¤È¤·¤Æ¼è¤ê¤Þ¤¹
! #  get_neighbors_by_gene('eco:b0002', 'all' 11, 10)

  --- get_best_best_neighbors_by_gene(genes_id, start, max_results)
***************
*** 804,817 ****
    get_paralogs_by_gene('eco:b0002', 11, 10)

! --- get_similarity_between_genes(genes_id1, genes_id2)
! 
! »ØÄê¤·¤¿£²¤Ä¤Î°äÅÁ»Ò´Ö¤Î Smith-Waterman ¥¹¥³¥¢¤ò´Þ¤à¥Ç¡¼¥¿¤òÊÖ¤·¤Þ¤¹¡£
! 
! ÌáÃÍ¡§
!   SSDBRelation
! 
! Îã¡§
!   # ÂçÄ²¶Ý¤Î b0002 °äÅÁ»Ò¤È b3940 °äÅÁ»Ò´Ö¤Î¥¹¥³¥¢¤ä¥¢¥é¥¤¥á¥ó¥ÈÎÎ°è¤òÆÀ¤ë
!   get_similarity_between_genes('eco:b0002', 'eco:b3940')

--- 835,848 ----
    get_paralogs_by_gene('eco:b0002', 11, 10)

! #--- get_similarity_between_genes(genes_id1, genes_id2)
! #
! #»ØÄê¤·¤¿£²¤Ä¤Î°äÅÁ»Ò´Ö¤Î Smith-Waterman ¥¹¥³¥¢¤ò´Þ¤à¥Ç¡¼¥¿¤òÊÖ¤·¤Þ¤¹¡£
! #
! #ÌáÃÍ¡§
! #  SSDBRelation
! #
! #Îã¡§
! #  # ÂçÄ²¶Ý¤Î b0002 °äÅÁ»Ò¤È b3940 °äÅÁ»Ò´Ö¤Î¥¹¥³¥¢¤ä¥¢¥é¥¤¥á¥ó¥ÈÎÎ°è¤òÆÀ¤ë
! #  get_similarity_between_genes('eco:b0002', 'eco:b3940')

***************
*** 833,840 ****
  --- get_genes_by_motifs(motif_id_list, start, max_results)

! »ØÄê¤·¤¿¥â¥Á¡¼¥Õ¤ò»ý¤Ä°äÅÁ»Ò¤ò¸¡º÷¤·¤Þ¤¹¡£

  ÌáÃÍ¡§
!   ArrayOfDefinition

  Îã¡§
--- 864,871 ----
  --- get_genes_by_motifs(motif_id_list, start, max_results)

! »ØÄê¤·¤¿¥â¥Á¡¼¥Õ¤òÁ´¤Æ»ý¤Ä°äÅÁ»Ò¤ò¸¡º÷¤·¤Þ¤¹¡£

  ÌáÃÍ¡§
!   ArrayOfDefinition (genes_id, definition)

  Îã¡§
***************
*** 856,860 ****

  ÌáÃÍ¡§
!   ArrayOfstring

  Îã¡§
--- 887,891 ----

  ÌáÃÍ¡§
!   ArrayOfstring (ko_id)

  Îã¡§
***************
*** 862,875 ****
    get_ko_by_gene('eco:b0002')

! --- get_ko_members(ko_id)

! »ØÄê¤·¤¿ ko_id ¤Î KO ¥¨¥ó¥È¥ê¤Ë´Þ¤Þ¤ì¤ë°äÅÁ»Ò¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£

  ÌáÃÍ¡§
!   ArrayOfstring

  Îã¡§
!   # KO ÈÖ¹æ K02208 ¤Î¥¢¥µ¥¤¥ó¤µ¤ì¤Æ¤¤¤ë°äÅÁ»Ò¤Î¥ê¥¹¥È
!   get_ko_by_gene('ko:K02598')

  --- get_oc_members_by_gene(genes_id, start, max_results)
--- 893,943 ----
    get_ko_by_gene('eco:b0002')

! #--- get_ko_members(ko_id)
! #
! #»ØÄê¤·¤¿ ko_id ¤Î KO ¥¨¥ó¥È¥ê¤Ë´Þ¤Þ¤ì¤ë°äÅÁ»Ò¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
! #
! #ÌáÃÍ¡§
! #  ArrayOfstring (genes_id)
! #
! #Îã¡§
! #  # KO ÈÖ¹æ K02208 ¤Î¥¢¥µ¥¤¥ó¤µ¤ì¤Æ¤¤¤ë°äÅÁ»Ò¤Î¥ê¥¹¥È
! #  get_ko_by_gene('ko:K02598')

! --- get_ko_by_ko_class(ko_class_id)
! 
! »ØÄê¤·¤¿ ko_class_id ¤Ë´Þ¤Þ¤ì¤ë ko_id ¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£

  ÌáÃÍ¡§
!   ArrayOfDefinition (ko_id)

  Îã¡§
!   # KO class '01196' ¤Ë´Þ¤Þ¤ì¤ë KO ¤Î¥ê¥¹¥È
!   get_ko_by_ko_class('01196')
! 
! --- get_genes_by_ko_class(ko_class_id, org, start, max_results)
! 
! »ØÄê¤·¤¿À¸Êª¼ï¤Î ko_class_id ¤Ë´Þ¤Þ¤ì¤ë°äÅÁ»Ò¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
! 
!  ÌáÃÍ¡§
!   ArrayOfDefinition (genes_id, definition)
! 
! Îã¡§
!   # KO ¥¯¥é¥¹ '00930' ¤Ë´Þ¤Þ¤ì¤ë¥Ò¥È°äÅÁ»Ò¤Î¥ê¥¹¥È
!   get_genes_by_ko_class('00903', 'hsa' , 1, 100)
! 
! --- get_genes_by_ko(ko_id, org)
! 
! »ØÄê¤·¤¿À¸Êª¼ï¤Î ko_id ¤Ë´Þ¤Þ¤ì¤ë°äÅÁ»Ò¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
! À¸Êª¼ï¥³¡¼¥É¤Ë all ¤ò»ØÄê¤¹¤ë¤ÈÁ´À¸Êª¼ï¤Î°äÅÁ»Ò¤òÊÖ¤·¤Þ¤¹¡£
! 
! ÌáÃÍ¡§
!   ArrayOfDefinition (genes_id, definition)
! 
! Îã¡§
!   # KO ÈÖ¹æ 'K00001' ¤Ë´Þ¤Þ¤ì¤ëÂçÄ²¶Ý°äÅÁ»Ò¤Î¥ê¥¹¥È
!   get_genes_by_ko('ko:K00010', 'eco')
! 
!   # KO ÈÖ¹æ 'K00010' ¤Ë´Þ¤Þ¤ì¤ëÁ´À¸Êª¼ï¤Î°äÅÁ»Ò¥ê¥¹¥È
!   get_genes_by_ko('ko:K00010', 'all')

  --- get_oc_members_by_gene(genes_id, start, max_results)
***************
*** 878,882 ****

  ÌáÃÍ¡§
!   ArrayOfstring

  Îã¡§
--- 946,950 ----

  ÌáÃÍ¡§
!   ArrayOfstring (genes_id)

  Îã¡§
***************
*** 890,894 ****

  ÌáÃÍ¡§
!   ArrayOfstring

  Îã¡§
--- 958,962 ----

  ÌáÃÍ¡§
!   ArrayOfstring (genes_id)

  Îã¡§
***************
*** 914,918 ****

  ÌáÃÍ¡§
!   string

  Îã¡§
--- 982,986 ----

  ÌáÃÍ¡§
!   string (URL)

  Îã¡§
***************
*** 930,934 ****

  ÌáÃÍ¡§
!   string

  Îã¡§
--- 998,1002 ----

  ÌáÃÍ¡§
!   string (URL)

  Îã¡§
***************
*** 941,944 ****
--- 1009,1043 ----
    color_pathway_by_objects('path:eco00053', obj_list, fg_list, bg_list)

+ --- get_html_of_marked_pathway_by_objects(pathway_id, object_id_list)
+ 
+ ²èÁü¤ÎÂå¤ï¤ê¤Ë¥¯¥ê¥Ã¥«¥Ö¥ë¥Þ¥Ã¥×¤ò´Þ¤à HTML ¥Ú¡¼¥¸¤Î URL ¤òÊÖ¤¹
+ ¥Ð¡¼¥¸¥ç¥ó¤Î 'mark_pathway_by_objects' ¥á¥½¥Ã¥É¤Ç¤¹¡£
+ 
+ ÌáÃÍ¡§
+   string (URL)
+ 
+ Îã¡§
+   # ÂçÄ²¶Ý¤Î¥Ñ¥¹¥¦¥§¥¤ '00970' ¤Î¡¢°äÅÁ»Ò 'eco:b4258'¡¢²½¹çÊª 'cpd:C00135'
+   # KO ÈÖ¹æ 'ko:K01881' ¤ËÀÖ¿§¤Ç¥Þ¡¼¥¯¤ò¤Ä¤±¤¿²èÁü¤Î¥¯¥ê¥Ã¥«¥Ö¥ë¥Þ¥Ã¥×¤ò
+   # É½¼¨¤¹¤ë HTML ¤Î URL ¤òÊÖ¤¹
+   obj_list = ['eco:b4258', 'cpd:C00135', 'ko:K01881']
+   get_html_of_marked_pathway_by_objects('path:eco00970', obj_list)
+ 
+ --- get_html_of_colored_pathway_by_objects(pathway_id, object_id_list, fg_color_list, bg_color_list)
+ 
+ ²èÁü¤ÎÂå¤ï¤ê¤Ë¥¯¥ê¥Ã¥«¥Ö¥ë¥Þ¥Ã¥×¤ò´Þ¤à HTML ¥Ú¡¼¥¸¤Î URL ¤òÊÖ¤¹
+ ¥Ð¡¼¥¸¥ç¥ó¤Î 'color_pathway_by_object' ¥á¥½¥Ã¥É¤Ç¤¹¡£
+ 
+ ÌáÃÍ¡§
+   string (URL)
+ 
+ Îã¡§
+   # ÂçÄ²¶Ý¤Î¥Ñ¥¹¥¦¥§¥¤ '00970' ¤Î¡¢°äÅÁ»Ò 'eco:b4258' ¤òÀÖÃÏ¤Ë³¥¿§¡¢²½¹çÊª
+   # 'cpd:C00135' ¤ò²«¿§ÃÏ¤ËÎÐ¡¢KO ÈÖ¹æ 'ko:K01881' ¤òÜôÃÏ¤ËÀÄ¤Î¿§¤Å¤±¤ò¤·¤¿
+   # ²èÁü¤Î¥¯¥ê¥Ã¥«¥Ö¥ë¥Þ¥Ã¥×¤òÉ½¼¨¤¹¤ë HTML ¤Î URL ¤òÊÖ¤¹
+   obj_list = ['eco:b4258', 'cpd:C00135', 'ko:K01881']
+   fg_list  = ['gray', '#00ff00', 'blue']
+   bg_list  = ['#ff0000', 'yellow', 'orange']
+   get_html_of_colored_pathway_by_objects('path:eco00970', obj_list, fg_list, bg_list)

  + ¥Ñ¥¹¥¦¥§¥¤¾å¤Î¥ª¥Ö¥¸¥§¥¯¥È¸¡º÷
***************
*** 950,954 ****

  ÌáÃÍ¡§
!   ArrayOfstring

  Îã¡§
--- 1049,1053 ----

  ÌáÃÍ¡§
!   ArrayOfstring (genes_id)

  Îã¡§
***************
*** 961,968 ****

  ÌáÃÍ¡§
!   ArrayOfstring

  Îã¡§
!   # ¥Ñ¥¹¥¦¥§¥¤ 00020 ÈÖ¤ËºÜ¤Ã¤Æ¤¤¤ë¹ÚÁÇÈÖ¹æ¤Î¥ê¥¹¥È
    get_enzymes_by_pathway('path:eco00020')

--- 1060,1067 ----

  ÌáÃÍ¡§
!   ArrayOfstring (enzyme_id)

  Îã¡§
!   # ÂçÄ²¶Ý¤Î¥Ñ¥¹¥¦¥§¥¤ 00020 ÈÖ¤ËºÜ¤Ã¤Æ¤¤¤ë¹ÚÁÇÈÖ¹æ¤Î¥ê¥¹¥È
    get_enzymes_by_pathway('path:eco00020')

***************
*** 972,981 ****

  ÌáÃÍ¡§
!   ArrayOfstring

  Îã¡§
!   # ¥Ñ¥¹¥¦¥§¥¤ 00020 ¤ËºÜ¤Ã¤Æ¤¤¤ë²½¹çÊª¤Î¥ê¥¹¥È
    get_compounds_by_pathway('path:eco00020')

  --- get_reactions_by_pathway(pathway_id)

--- 1071,1091 ----

  ÌáÃÍ¡§
!   ArrayOfstring (compound_id)

  Îã¡§
!   # ÂçÄ²¶Ý¤Î¥Ñ¥¹¥¦¥§¥¤ 00020 ¤ËºÜ¤Ã¤Æ¤¤¤ë²½¹çÊª¤Î¥ê¥¹¥È
    get_compounds_by_pathway('path:eco00020')

+ --- get_glycans_by_pathway(pathway_id)
+ 
+ »ØÄê¤·¤¿¥Ñ¥¹¥¦¥§¥¤¤ËºÜ¤Ã¤Æ¤¤¤ëÅüº¿¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
+ 
+ ÌáÃÍ¡§
+   ArrayOfstring (glycan_id)
+ 
+ Îã¡§
+   # ÂçÄ²¶Ý¤Î¥Ñ¥¹¥¦¥§¥¤ 00510 ¤ËºÜ¤Ã¤Æ¤¤¤ëÅüº¿¤Î¥ê¥¹¥È
+   get_glycans_by_pathway('path:eco00510')
+ 
  --- get_reactions_by_pathway(pathway_id)

***************
*** 983,991 ****

  ÌáÃÍ¡§
!   ArrayOfstring

  Îã¡§
!   # ¥Ñ¥¹¥¦¥§¥¤ 00260 ÈÖ¤ËºÜ¤Ã¤Æ¤¤¤ë¥ê¥¢¥¯¥·¥ç¥ó¤Î¥ê¥¹¥È
!   get_reactions_by_pathways('path:map00260')

--- 1093,1113 ----

  ÌáÃÍ¡§
!   ArrayOfstring (reaction_id)

  Îã¡§
!   # ÂçÄ²¶Ý¤Î¥Ñ¥¹¥¦¥§¥¤ 00260 ÈÖ¤ËºÜ¤Ã¤Æ¤¤¤ë¥ê¥¢¥¯¥·¥ç¥ó¤Î¥ê¥¹¥È
!   get_reactions_by_pathways('path:eco00260')
! 
! --- get_kos_by_pathway(pathway_id)
! 
! »ØÄê¤·¤¿¥Ñ¥¹¥¦¥§¥¤¤ËºÜ¤Ã¤Æ¤¤¤ë KO ÈÖ¹æ¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
! 
! ÌáÃÍ¡§
!   ArrayOfstring (ko_id)
! 
! Îã¡§
!   # ¥Ò¥È¤Î¥Ñ¥¹¥¦¥§¥¤ 00010 ¤ËºÜ¤Ã¤Æ¤¤¤ë KO ÈÖ¹æ¤Î¥ê¥¹¥È
!   get_kos_by_pathway('path:hsa00010')
! 

***************
*** 997,1001 ****

  ÌáÃÍ¡§
!   ArrayOfstring

  Îã¡§
--- 1119,1123 ----