[BioRuby-cvs] bioruby/doc KEGG_API.rd, 1.1, 1.2 KEGG_API.rd.ja, 1.7, 1.8
Katayama Toshiaki
k at pub.open-bio.org
Thu Feb 23 04:51:25 UTC 2006
Update of /home/repository/bioruby/bioruby/doc
In directory pub.open-bio.org:/tmp/cvs-serv4725/doc
Modified Files:
KEGG_API.rd KEGG_API.rd.ja
Log Message:
* updated for KEGG API v5.0
Index: KEGG_API.rd.ja
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/KEGG_API.rd.ja,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** KEGG_API.rd.ja 31 Aug 2005 13:29:01 -0000 1.7
--- KEGG_API.rd.ja 23 Feb 2006 04:51:23 -0000 1.8
***************
*** 1,7 ****
=begin
!
! $Id$
!
! Copyright (C) 2003-2005 Toshiaki Katayama <k at bioruby.org>
= KEGG API
--- 1,7 ----
=begin
!
! $Id$
!
! Copyright (C) 2003-2006 Toshiaki Katayama <k at bioruby.org>
= KEGG API
***************
*** 30,33 ****
--- 30,34 ----
* ((<Definition ·¿>)), ((<ArrayOfDefinition ·¿>))
* ((<LinkDBRelation ·¿>)), ((<ArrayOfLinkDBRelation ·¿>))
+ * ((<PathwayElement ·¿>)), ((<ArrayOfPathwayElement ·¿>))
* ((<¥á¥½¥Ã¥É°ìÍ÷>))
* ((<¥á¥¿¾ðÊó>))
***************
*** 39,45 ****
((<bfind>)),
((<bget>)),
! ((<btit>))
* ((<LinkDB>))
* ((<get_linkdb_by_entry>))
* ((<SSDB>))
* ((<get_best_best_neighbors_by_gene>)),
--- 40,59 ----
((<bfind>)),
((<bget>)),
! ((<btit>)),
! ((<bconv>))
* ((<LinkDB>))
* ((<get_linkdb_by_entry>))
+ * ((<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>))
* ((<SSDB>))
* ((<get_best_best_neighbors_by_gene>)),
***************
*** 63,69 ****
* ((<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>)),
--- 77,86 ----
* ((<mark_pathway_by_objects>)),
((<color_pathway_by_objects>)),
+ ((<color_pathway_by_elements>)),
((<get_html_of_marked_pathway_by_objects>)),
! ((<get_html_of_colored_pathway_by_objects>)),
! ((<get_html_of_colored_pathway_by_elements>))
! * ((<get_elements_by_pathway>)),
! ((<get_genes_by_pathway>)),
((<get_enzymes_by_pathway>)),
((<get_compounds_by_pathway>)),
***************
*** 78,93 ****
((<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>))
--- 95,98 ----
***************
*** 634,637 ****
--- 639,654 ----
Ê£¿ô¤Î LinkDBRelation ·¿¥Ç¡¼¥¿¤ò´Þ¤àÇÛÎó¤Ç¤¹¡£
+ + PathwayElement ·¿
+
+ element_id ¥Ñ¥¹¥¦¥§¥¤¾å¤Î¥ª¥Ö¥¸¥§¥¯¥È¤ò»Ø¤¹¥æ¥Ë¡¼¥¯¤Ê ID (int)
+ type ¥ª¥Ö¥¸¥§¥¯¥È¤Î¼ïÎà ("gene", "enzyme" ¤Ê¤É) (string)
+ names ¥ª¥Ö¥¸¥§¥¯¥È¤Ë¤Ä¤±¤é¤ì¤¿Ì¾Á°¤Î¥ê¥¹¥È (ArrayOfstring)
+ components ¥°¥ë¡¼¥×¤Î¾ì¹ç¤Ê¤É´Þ¤Þ¤ì¤ë¥ª¥Ö¥¸¥§¥¯¥È¤Î¥ê¥¹¥È (ArrayOfint)
+
+ + ArrayOfPathwayElement ·¿
+
+ Ê£¿ô¤Î PathwayElement ·¿¥Ç¡¼¥¿¤ò´Þ¤àÇÛÎó¤Ç¤¹¡£
+
+
=== ¥á¥½¥Ã¥É°ìÍ÷
***************
*** 740,743 ****
--- 757,772 ----
btit("hsa:1798 mmu:13478 dme:CG5287-PA cel:Y60A3A.14")
+ --- bconv(string)
+
+ ³°Éô¥Ç¡¼¥¿¥Ù¡¼¥¹¤Î ID ¤ò KEGG ¤Î ID ¤ËÊÑ´¹¤·¤Þ¤¹¡£Âбþ¤·¤Æ¤¤¤ë³°Éô¥Ç¡¼¥¿
+ ¥Ù¡¼¥¹¤Ï NCBI Gene ID, NCBI GI, GenBank ID, UniProt ID ¤Ç¤¹¡£
+ ·ë²Ì¤Ï¡¢£±¹ÔËè¤ËÌ䤤¹ç¤ï¤» ID ¤ÈÊÑ´¹ ID ¤Î¥¿¥ÖÀÚ¤êʸ»úÎó¤È¤·¤ÆÊÖ¤µ¤ì¤Þ¤¹¡£
+
+ ÌáÃÍ¡§
+ string
+
+ Î㡧
+ # NCBI GI ¤È Gene ID ¤ò KEGG genes_id ¤ËÊÑ´¹
+ serv.bconv("ncbi-gi:10047086 ncbi-gi:10047090 ncbi-geneid:14751")
==== LinkDB
***************
*** 756,759 ****
--- 785,925 ----
get_linkdb_by_entry('eco:b0002', 'pathway', 11, 10)
+ + °äÅÁ»Ò¤È¹ÚÁÇÈÖ¹æ¤Î´Ø·¸
+
+ --- get_genes_by_enzyme(enzyme_id, org)
+
+ ÂоÝÀ¸Êª¼ï¤Ë¤ª¤¤¤Æ¡¢»ØÄꤷ¤¿¹ÚÁÇÈÖ¹æ¤ò»ý¤Ä°äÅÁ»Ò¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
+
+ ÌáÃÍ¡§
+ ArrayOfstring (genes_id)
+
+ Î㡧
+ # ¹ÚÁÇÈÖ¹æ 1.1.1.1 ¤ò»ý¤ÄÂçIJ¶Ý¤Î°äÅÁ»Ò¤Î¥ê¥¹¥È
+ get_genes_by_enzyme('ec:1.1.1.1', 'eco')
+
+ --- get_enzymes_by_gene(genes_id)
+
+ »ØÄꤷ¤¿°äÅÁ»Ò¤ËÂбþ¤¹¤ë¹ÚÁÇÈÖ¹æ¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
+
+ ÌáÃÍ¡§
+ ArrayOfstring (enzyme_id)
+
+ Î㡧
+ # ÂçIJ¶Ý°äÅÁ»Ò 'eco:b0002' ¤Î¹ÚÁÇÈÖ¹æ¤Î¥ê¥¹¥È
+ get_enzymes_by_gene(eco:b0002)
+
+
+ + ¹ÚÁÇ¡¢²½¹çʪ¡¢¥ê¥¢¥¯¥·¥ç¥ó¤Î´Ø·¸
+
+ --- get_enzymes_by_compound(compound_id)
+
+ »ØÄꤷ¤¿²½¹çʪ¤ËÂбþ¤¹¤ë¹ÚÁÇÈÖ¹æ¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
+
+ ÌáÃÍ¡§
+ ArrayOfstring (compound_id)
+
+ Î㡧
+ # ²½¹çʪ 'cpd:C00345' ¤ÎÂå¼Õ¤Ë´Ø¤ï¤ë¹ÚÁǤΥꥹ¥È
+ get_enzymes_by_compound('cpd:C00345')
+
+ --- get_enzymes_by_glycan(compound_id)
+
+ »ØÄꤷ¤¿Åüº¿¤ËÂбþ¤¹¤ë¹ÚÁÇÈÖ¹æ¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
+
+ ÌáÃÍ¡§
+ ArrayOfstring (glycan_id)
+
+ Î㡧
+ # Åüº¿ 'gl:G00001' ¤ÎÂå¼Õ¤Ë´Ø¤ï¤ë¹ÚÁǤΥꥹ¥È
+ get_enzymes_by_glycan('gl:G00001')
+
+ --- get_enzymes_by_reaction(reaction_id)
+
+ »ØÄꤷ¤¿¥ê¥¢¥¯¥·¥ç¥óÈÖ¹æ¤ËÂбþ¤¹¤ë¹ÚÁÇÈÖ¹æ¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
+
+ ÌáÃÍ¡§
+ ArrayOfstring (reaction_id)
+
+ Î㡧
+ # ¥ê¥¢¥¯¥·¥ç¥óÈÖ¹æ R00100 ¤ò»ý¤Ä¹ÚÁǤΥꥹ¥È
+ get_enzymes_by_reaction('rn:R00100')
+
+ --- get_compounds_by_enzyme(enzyme_id)
+
+ »ØÄꤷ¤¿¹ÚÁÇÈÖ¹æ¤ËÂбþ¤¹¤ë²½¹çʪ¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
+
+ ÌáÃÍ¡§
+ ArrayOfstring (compound_id)
+
+ Î㡧
+ # ¹ÚÁÇÈÖ¹æ 'ec:2.7.1.12' ¤ÎÂå¼Õ¤Ë´Ø¤ï¤ë²½¹çʪ¤Î¥ê¥¹¥È
+ get_compounds_by_enzyme('ec:2.7.1.12')
+
+ --- get_compounds_by_reaction(reaction_id)
+
+ »ØÄꤷ¤¿¥ê¥¢¥¯¥·¥ç¥ó¤ËÂбþ¤¹¤ë²½¹çʪ¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
+
+ ÌáÃÍ¡§
+ ArrayOfstring (compound_id)
+
+ Î㡧
+ # ¥ê¥¢¥¯¥·¥ç¥óÈÖ¹æ 'rn:R00100' ¤ÎÈ¿±þ¤Ë´Ø¤ï¤ë²½¹çʪ¤Î¥ê¥¹¥È
+ get_compounds_by_reaction('rn:R00100')
+
+ --- get_glycans_by_enzyme(enzyme_id)
+
+ »ØÄꤷ¤¿¹ÚÁÇÈÖ¹æ¤ËÂбþ¤¹¤ëÅüº¿¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
+
+ ÌáÃÍ¡§
+ ArrayOfstring (glycan_id)
+
+ Î㡧
+ # ¹ÚÁÇÈÖ¹æ 'ec:2.4.1.141' ¤ÎÂå¼Õ¤Ë´Ø¤ï¤ëÅüº¿¤Î¥ê¥¹¥È
+ get_glycans_by_enzyme('ec:2.4.1.141')
+
+ --- get_glycans_by_reaction(reaction_id)
+
+ »ØÄꤷ¤¿¥ê¥¢¥¯¥·¥ç¥ó¤ËÂбþ¤¹¤ëÅüº¿¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
+
+ ÌáÃÍ¡§
+ ArrayOfstring (glycan_id)
+
+ Î㡧
+ # ¥ê¥¢¥¯¥·¥ç¥óÈÖ¹æ 'rn:R06164' ¤ÎÈ¿±þ¤Ë´Ø¤ï¤ëÅüº¿¤Î¥ê¥¹¥È
+ get_glycans_by_reaction('rn:R06164')
+
+ --- get_reactions_by_enzyme(enzyme_id)
+
+ »ØÄꤷ¤¿¹ÚÁÇÈÖ¹æ¤ËÂбþ¤¹¤ë¥ê¥¢¥¯¥·¥ç¥ó¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
+
+ ÌáÃÍ¡§
+ ArrayOfstring (reaction_id)
+
+ Î㡧
+ # ¹ÚÁÇÈÖ¹æ 'ec:2.7.1.12' ¤ÎÈ¿±þ¤Ë´Ø¤ï¤ë¥ê¥¢¥¯¥·¥ç¥óÈÖ¹æ¤Î¥ê¥¹¥È
+ get_reactions_by_enzyme('ec:2.7.1.12')
+
+ --- get_reactions_by_compound(compound_id)
+
+ »ØÄꤷ¤¿²½¹çʪ¤ËÂбþ¤¹¤ë¥ê¥¢¥¯¥·¥ç¥ó¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
+
+ ÌáÃÍ¡§
+ ArrayOfstring (reaction_id)
+
+ Î㡧
+ # ²½¹çʪ 'cpd:C00199' ¤Î¿¨ÇÞÈ¿±þ¤Ë´Ø¤ï¤ë¥ê¥¢¥¯¥·¥ç¥óÈÖ¹æ¤Î¥ê¥¹¥È
+ get_reactions_by_compound('cpd:C00199')
+
+ --- get_reactions_by_glycan(glycan_id)
+
+ »ØÄꤷ¤¿Åüº¿¤ËÂбþ¤¹¤ë¥ê¥¢¥¯¥·¥ç¥ó¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
+
+ ÌáÃÍ¡§
+ ArrayOfstring (reaction_id)
+
+ Î㡧
+ # Åüº¿ 'gl:G00001' ¤Î¿¨ÇÞÈ¿±þ¤Ë´Ø¤ï¤ë¥ê¥¢¥¯¥·¥ç¥óÈÖ¹æ¤Î¥ê¥¹¥È
+ get_reactions_by_glycan('gl:G00001')
+
==== SSDB
***************
*** 1009,1012 ****
--- 1175,1217 ----
color_pathway_by_objects('path:eco00053', obj_list, fg_list, bg_list)
+ --- color_pathway_by_elements(pathway_id, element_id_list, fg_color_list, bg_color_list)
+
+ »ØÄꤷ¤¿ element_id ¤ËÂбþ¤¹¤ë¥Ñ¥¹¥¦¥§¥¤¾å¤Î¥ª¥Ö¥¸¥§¥¯¥È¡ÊĹÊý·Á¤ä´Ý¤Ê¤É¡Ë
+ ¤ËÂФ·¡¢Ê¸»ú¤ÈÏÈ¤Ë fg_color_list ¤Ç»ØÄꤷ¤¿¿§¡¢ÇØ·Ê¤Ë bg_color_list ¤Ç
+ »ØÄꤷ¤¿¿§¤ò¤Ä¤±¤¿²èÁü¤òÀ¸À®¡¢²èÁü¤Î URL ¤òÊÖ¤·¤Þ¤¹¡£object_id_list ¤È
+ fg_color_list, bg_color_list ¤ÎÍ×ÁǤοô¤È½çÈÖ¤ò·¤¨¤ë¤è¤¦¤ËÃí°Õ¤¹¤ë
+ ɬÍפ¬¤¢¤ê¤Þ¤¹¡£
+
+ KEGG PATHWAY ¤Ç¤Ï¡¢Ê£¿ô¤Î°äÅÁ»Ò¤¬°ì¤Ä¤Î¥Ü¥Ã¥¯¥¹¤Ë³ä¤êÅö¤Æ¤é¤ì¤Æ¤¤¤¿¤ê¡¢
+ µÕ¤Ë£±¤Ä¤Î°äÅÁ»Ò¤¬Ê£¿ô¤Î¥Ü¥Ã¥¯¥¹¤Ë³ä¤êÅö¤Æ¤é¤ì¤Æ¤¤¤ë¤³¤È¤¬¤¢¤ê¤Þ¤¹¡£
+ ¤³¤Î¤è¤¦¤Ê¾ì¹ç color_pathway_by_objects ¥á¥½¥Ã¥É¤Ç¤ÏÅɤêʬ¤±¤ë¤³¤È¤¬
+ ½ÐÍè¤Þ¤»¤ó¤¬¡¢color_pathway_by_elements ¤ò»È¤¦¤³¤È¤Ç²ò·è¤Ç¤¤Þ¤¹¡£
+
+ element_id ¤Ï KEGG PATHWAY ¤Î XML ɽ¸½¤Ç¤¢¤ë KGML ¤Î <entry> ¥¿¥°¤Ç
+ »ØÄꤵ¤ì¤ë¡¢¥Ñ¥¹¥¦¥§¥¤¾å¤Î¥°¥é¥Õ¥£¥«¥ë¤ÊÍ×ÁÇËè¤Ë¤Ä¤±¤é¤ì¤¿¥æ¥Ë¡¼¥¯¤Ê
+ ¿ôÃͤǤ¹¡£¥Ñ¥¹¥¦¥§¥¤¾å¤Î element_id ¤Ï get_elements_by_pathway ¥á¥½¥Ã¥É¤Ç
+ PathwayElement ¥ª¥Ö¥¸¥§¥¯¥È¤Î¥ê¥¹¥È¤È¤·¤ÆÆÀ¤ë¤³¤È¤¬¤Ç¤¤Þ¤¹¡£
+ PathwayElement ¤Î type ¤ä name °À¤Ë¤è¤ê°äÅÁ»Ò¡¢¹ÚÁÇ¡¢²½¹çʪ¤Ê¤É¤È
+ Âбþ¤ò¼è¤ê¡¢element_id ¤ÎÃͤò»È¤Ã¤Æ¥ª¥Ö¥¸¥§¥¯¥È¤òÆÃÄꤷ¤Þ¤¹¡£
+
+ KGML ¤Ë¤Ä¤¤¤Æ¾Ü¤·¤¯¤Ï²¼µ¤Î¥Ú¡¼¥¸¤ò»²¾È¤·¤Æ¤¯¤À¤µ¤¤¡£
+
+ * ((<URL:http://www.genome.jp/kegg/xml/>))
+
+ Ìá¤êÃÍ¡§
+ string (URL)
+
+ Î㡧
+ # ¸ÏÁð¶Ý¤Î¥Ñ¥¹¥¦¥§¥¤ path:bsu00010 ¾å¤ËºÜ¤Ã¤Æ¤¤¤ë¡¢
+ # °äÅÁ»Ò bsu:BG11350 (element_id 78, ec:3.2.1.86) ¤òÀÖÏÈ/²«ÇطʤÇ
+ # °äÅÁ»Ò bsu:BG11203 (element_id 79, ec:3.2.1.86) ¤òÀÄÏÈ/²«ÇطʤÇ
+ # °äÅÁ»Ò bsu:BG11685 (element_id 51, ec:2.7.1.2) ¤òÀÖÏÈ/ÜôÇطʤÇ
+ # °äÅÁ»Ò bsu:BG11685 (element_id 47, ec:2.7.1.2) ¤òÀÄÏÈ/ÜôÇطʤÇ
+ # ¤½¤ì¤¾¤ìÃ忧¤·¤¿²èÁü¤Î URL ¤òÊÖ¤·¤Þ¤¹¡£
+ element_id_list = [ 78, 79, 51, 47 ]
+ fg_list = [ '#ff0000', '#0000ff', '#ff0000', '#0000ff' ]
+ bg_list = [ '#ffff00', '#ffff00', '#ffcc00', '#ffcc00' ]
+ color_pathway_by_elements('path:bsu00010', element_id_list, fg_list, bg_list)
+
--- get_html_of_marked_pathway_by_objects(pathway_id, object_id_list)
***************
*** 1027,1031 ****
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¡§
--- 1232,1236 ----
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_objects' ¥á¥½¥Ã¥É¤Ç¤¹¡£
ÌáÃÍ¡§
***************
*** 1041,1046 ****
--- 1246,1296 ----
get_html_of_colored_pathway_by_objects('path:eco00970', obj_list, fg_list, bg_list)
+ --- get_html_of_colored_pathway_by_elements(pathway_id, element_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_elements' ¥á¥½¥Ã¥É¤Ç¤¹¡£
+
+ ÌáÃÍ¡§
+ string (URL)
+
+ Î㡧
+ # ¸ÏÁð¶Ý¤Î¥Ñ¥¹¥¦¥§¥¤ path:bsu00010 ¾å¤ËºÜ¤Ã¤Æ¤¤¤ë¡¢
+ # °äÅÁ»Ò bsu:BG11350 (element_id 78, ec:3.2.1.86) ¤òÀÖÏÈ/²«ÇطʤÇ
+ # °äÅÁ»Ò bsu:BG11203 (element_id 79, ec:3.2.1.86) ¤òÀÄÏÈ/²«ÇطʤÇ
+ # °äÅÁ»Ò bsu:BG11685 (element_id 51, ec:2.7.1.2) ¤òÀÖÏÈ/ÜôÇطʤÇ
+ # °äÅÁ»Ò bsu:BG11685 (element_id 47, ec:2.7.1.2) ¤òÀÄÏÈ/ÜôÇطʤÇ
+ # Ã忧¤·¤¿²èÁü¤Î¥¯¥ê¥Ã¥«¥Ö¥ë¥Þ¥Ã¥×¤òɽ¼¨¤¹¤ë HTML ¤Î URL ¤òÊÖ¤·¤Þ¤¹¡£
+ element_id_list = [ 78, 79, 51, 47 ]
+ fg_list = [ '#ff0000', '#0000ff', '#ff0000', '#0000ff' ]
+ bg_list = [ '#ffff00', '#ffff00', '#ffcc00', '#ffcc00' ]
+ color_pathway_by_elements('path:bsu00010', element_id_list, fg_list, bg_list)
+
+ ¥Ñ¥¹¥¦¥§¥¤¾å¤Î¥ª¥Ö¥¸¥§¥¯¥È¸¡º÷
+ --- get_elements_by_pathway(pathway_id)
+
+ »ØÄꤷ¤¿¥Ñ¥¹¥¦¥§¥¤¾å¤ËºÜ¤Ã¤Æ¤¤¤ë¥ª¥Ö¥¸¥§¥¯¥ÈÍ×ÁǤΥꥹ¥È¤òÊÖ¤·¤Þ¤¹¡£
+ ÍøÍÑË¡¤Ë¤Ä¤¤¤Æ¤Ï color_pathway_by_elements ¥á¥½¥Ã¥É¤ò»²¾È¤·¤Æ¤¯¤À¤µ¤¤¡£
+
+ ÌáÃÍ¡§
+ ArrayOfPathwayElement
+
+ Î㡧
+ # ¸ÏÁð¶Ý¤Î¥Ñ¥¹¥¦¥§¥¤ path:bsu00010 ¾å¤ËºÜ¤Ã¤Æ¤¤¤ë PathwayElement ¤Î
+ # ¥ê¥¹¥È¤ò¼èÆÀ¤¹¤ë¡£
+ get_elements_by_pathway('path:bsu00010')
+
+ # Ruby ¤Ç°äÅÁ»Ò bsu:BG11350, bsu:BG11203 ¤È bsu:BG11685 ¤Î element_id ¤ò
+ # Ä´¤Ù¤ëÎã¡£
+ elems = serv.get_elements_by_pathway('path:bsu00010')
+ genes = [ 'bsu:BG11350', 'bsu:BG11203', 'bsu:BG11685' ]
+ elems.each do |elem|
+ genes.each do |gene|
+ if elem.names.include?(gene)
+ puts gene, elem.element_id
+ end
+ end
+ end
+
--- get_genes_by_pathway(pathway_id)
***************
*** 1097,1101 ****
Î㡧
# ÂçIJ¶Ý¤Î¥Ñ¥¹¥¦¥§¥¤ 00260 È֤˺ܤäƤ¤¤ë¥ê¥¢¥¯¥·¥ç¥ó¤Î¥ê¥¹¥È
! get_reactions_by_pathways('path:eco00260')
--- get_kos_by_pathway(pathway_id)
--- 1347,1351 ----
Î㡧
# ÂçIJ¶Ý¤Î¥Ñ¥¹¥¦¥§¥¤ 00260 È֤˺ܤäƤ¤¤ë¥ê¥¢¥¯¥·¥ç¥ó¤Î¥ê¥¹¥È
! get_reactions_by_pathway('path:eco00260')
--- get_kos_by_pathway(pathway_id)
***************
*** 1200,1341 ****
- + °äÅÁ»Ò¤È¹ÚÁÇÈÖ¹æ¤Î´Ø·¸
-
- --- get_genes_by_enzyme(enzyme_id, org)
-
- ÂоÝÀ¸Êª¼ï¤Ë¤ª¤¤¤Æ¡¢»ØÄꤷ¤¿¹ÚÁÇÈÖ¹æ¤ò»ý¤Ä°äÅÁ»Ò¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
-
- ÌáÃÍ¡§
- ArrayOfstring (genes_id)
-
- Î㡧
- # ¹ÚÁÇÈÖ¹æ 1.1.1.1 ¤ò»ý¤ÄÂçIJ¶Ý¤Î°äÅÁ»Ò¤Î¥ê¥¹¥È
- get_genes_by_enzyme('ec:1.1.1.1', 'eco')
-
- --- get_enzymes_by_gene(genes_id)
-
- »ØÄꤷ¤¿°äÅÁ»Ò¤ËÂбþ¤¹¤ë¹ÚÁÇÈÖ¹æ¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
-
- ÌáÃÍ¡§
- ArrayOfstring (enzyme_id)
-
- Î㡧
- # ÂçIJ¶Ý°äÅÁ»Ò 'eco:b0002' ¤Î¹ÚÁÇÈÖ¹æ¤Î¥ê¥¹¥È
- get_enzymes_by_gene(eco:b0002)
-
-
- + ¹ÚÁÇ¡¢²½¹çʪ¡¢¥ê¥¢¥¯¥·¥ç¥ó¤Î´Ø·¸
-
- --- get_enzymes_by_compound(compound_id)
-
- »ØÄꤷ¤¿²½¹çʪ¤ËÂбþ¤¹¤ë¹ÚÁÇÈÖ¹æ¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
-
- ÌáÃÍ¡§
- ArrayOfstring (compound_id)
-
- Î㡧
- # ²½¹çʪ 'cpd:C00345' ¤ÎÂå¼Õ¤Ë´Ø¤ï¤ë¹ÚÁǤΥꥹ¥È
- get_enzymes_by_compound('cpd:C00345')
-
- --- get_enzymes_by_glycan(compound_id)
-
- »ØÄꤷ¤¿Åüº¿¤ËÂбþ¤¹¤ë¹ÚÁÇÈÖ¹æ¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
-
- ÌáÃÍ¡§
- ArrayOfstring (glycan_id)
-
- Î㡧
- # Åüº¿ 'gl:G00001' ¤ÎÂå¼Õ¤Ë´Ø¤ï¤ë¹ÚÁǤΥꥹ¥È
- get_enzymes_by_glycan('gl:G00001')
-
- --- get_enzymes_by_reaction(reaction_id)
-
- »ØÄꤷ¤¿¥ê¥¢¥¯¥·¥ç¥óÈÖ¹æ¤ËÂбþ¤¹¤ë¹ÚÁÇÈÖ¹æ¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
-
- ÌáÃÍ¡§
- ArrayOfstring (reaction_id)
-
- Î㡧
- # ¥ê¥¢¥¯¥·¥ç¥óÈÖ¹æ R00100 ¤ò»ý¤Ä¹ÚÁǤΥꥹ¥È
- get_enzymes_by_reaction('rn:R00100')
-
- --- get_compounds_by_enzyme(enzyme_id)
-
- »ØÄꤷ¤¿¹ÚÁÇÈÖ¹æ¤ËÂбþ¤¹¤ë²½¹çʪ¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
-
- ÌáÃÍ¡§
- ArrayOfstring (compound_id)
-
- Î㡧
- # ¹ÚÁÇÈÖ¹æ 'ec:2.7.1.12' ¤ÎÂå¼Õ¤Ë´Ø¤ï¤ë²½¹çʪ¤Î¥ê¥¹¥È
- get_compounds_by_enzyme('ec:2.7.1.12')
-
- --- get_compounds_by_reaction(reaction_id)
-
- »ØÄꤷ¤¿¥ê¥¢¥¯¥·¥ç¥ó¤ËÂбþ¤¹¤ë²½¹çʪ¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
-
- ÌáÃÍ¡§
- ArrayOfstring (compound_id)
-
- Î㡧
- # ¥ê¥¢¥¯¥·¥ç¥óÈÖ¹æ 'rn:R00100' ¤ÎÈ¿±þ¤Ë´Ø¤ï¤ë²½¹çʪ¤Î¥ê¥¹¥È
- get_compounds_by_reaction('rn:R00100')
-
- --- get_glycans_by_enzyme(enzyme_id)
-
- »ØÄꤷ¤¿¹ÚÁÇÈÖ¹æ¤ËÂбþ¤¹¤ëÅüº¿¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
-
- ÌáÃÍ¡§
- ArrayOfstring (glycan_id)
-
- Î㡧
- # ¹ÚÁÇÈÖ¹æ 'ec:2.4.1.141' ¤ÎÂå¼Õ¤Ë´Ø¤ï¤ëÅüº¿¤Î¥ê¥¹¥È
- get_glycans_by_enzyme('ec:2.4.1.141')
-
- --- get_glycans_by_reaction(reaction_id)
-
- »ØÄꤷ¤¿¥ê¥¢¥¯¥·¥ç¥ó¤ËÂбþ¤¹¤ëÅüº¿¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
-
- ÌáÃÍ¡§
- ArrayOfstring (glycan_id)
-
- Î㡧
- # ¥ê¥¢¥¯¥·¥ç¥óÈÖ¹æ 'rn:R06164' ¤ÎÈ¿±þ¤Ë´Ø¤ï¤ëÅüº¿¤Î¥ê¥¹¥È
- get_glycans_by_reaction('rn:R06164')
-
- --- get_reactions_by_enzyme(enzyme_id)
-
- »ØÄꤷ¤¿¹ÚÁÇÈÖ¹æ¤ËÂбþ¤¹¤ë¥ê¥¢¥¯¥·¥ç¥ó¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
-
- ÌáÃÍ¡§
- ArrayOfstring (reaction_id)
-
- Î㡧
- # ¹ÚÁÇÈÖ¹æ 'ec:2.7.1.12' ¤ÎÈ¿±þ¤Ë´Ø¤ï¤ë¥ê¥¢¥¯¥·¥ç¥óÈÖ¹æ¤Î¥ê¥¹¥È
- get_reactions_by_enzyme('ec:2.7.1.12')
-
- --- get_reactions_by_compound(compound_id)
-
- »ØÄꤷ¤¿²½¹çʪ¤ËÂбþ¤¹¤ë¥ê¥¢¥¯¥·¥ç¥ó¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
-
- ÌáÃÍ¡§
- ArrayOfstring (reaction_id)
-
- Î㡧
- # ²½¹çʪ 'cpd:C00199' ¤Î¿¨ÇÞÈ¿±þ¤Ë´Ø¤ï¤ë¥ê¥¢¥¯¥·¥ç¥óÈÖ¹æ¤Î¥ê¥¹¥È
- get_reactions_by_compound('cpd:C00199')
-
- --- get_reactions_by_glycan(glycan_id)
-
- »ØÄꤷ¤¿Åüº¿¤ËÂбþ¤¹¤ë¥ê¥¢¥¯¥·¥ç¥ó¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
-
- ÌáÃÍ¡§
- ArrayOfstring (reaction_id)
-
- Î㡧
- # Åüº¿ 'gl:G00001' ¤Î¿¨ÇÞÈ¿±þ¤Ë´Ø¤ï¤ë¥ê¥¢¥¯¥·¥ç¥óÈÖ¹æ¤Î¥ê¥¹¥È
- get_reactions_by_glycan('gl:G00001')
-
-
==== GENES
--- 1450,1453 ----
***************
*** 1395,1399 ****
== Notes
! Last updated: May 31, 2005
=end
--- 1507,1512 ----
== Notes
! Last updated: Feb 17, 2006
=end
+
Index: KEGG_API.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/KEGG_API.rd,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** KEGG_API.rd 31 Aug 2005 13:29:01 -0000 1.1
--- KEGG_API.rd 23 Feb 2006 04:51:23 -0000 1.2
***************
*** 3,7 ****
$Id$
! Copyright (C) 2003-2005 Toshiaki Katayama <k at bioruby.org>
= KEGG API
--- 3,7 ----
$Id$
! Copyright (C) 2003-2006 Toshiaki Katayama <k at bioruby.org>
= KEGG API
***************
*** 80,83 ****
--- 80,84 ----
* ((<Definition>)), ((<ArrayOfDefinition>))
* ((<LinkDBRelation>)), ((<ArrayOfLinkDBRelation>))
+ * ((<PathwayElement>)), ((<ArrayOfPathwayElement>))
* ((<Methods>))
* ((<Meta information>))
***************
*** 89,95 ****
((<bfind>)),
((<bget>)),
! ((<btit>))
* ((<LinkDB>))
* ((<get_linkdb_by_entry>))
* ((<SSDB>))
* ((<get_best_best_neighbors_by_gene>)),
--- 90,109 ----
((<bfind>)),
((<bget>)),
! ((<btit>)),
! ((<bconv>))
* ((<LinkDB>))
* ((<get_linkdb_by_entry>))
+ * ((<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>))
* ((<SSDB>))
* ((<get_best_best_neighbors_by_gene>)),
***************
*** 113,119 ****
* ((<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>)),
--- 127,136 ----
* ((<mark_pathway_by_objects>)),
((<color_pathway_by_objects>)),
+ ((<color_pathway_by_elements>)),
((<get_html_of_marked_pathway_by_objects>)),
! ((<get_html_of_colored_pathway_by_objects>)),
! ((<get_html_of_colored_pathway_by_elements>))
! * ((<get_elements_by_pathway>)),
! ((<get_genes_by_pathway>)),
((<get_enzymes_by_pathway>)),
((<get_compounds_by_pathway>)),
***************
*** 128,143 ****
((<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>))
--- 145,148 ----
***************
*** 508,513 ****
=== Terminology
! * 'org' is a three-letter organism code used in KEGG. The list can be
! found at (see the description of the list_organisms method below):
* ((<URL:http://www.genome.jp/kegg/catalog/org_list.html>))
--- 513,519 ----
=== Terminology
! * 'org' is a three-letter (or four-letter) organism code used in KEGG.
! The list can be found at (see the description of the list_organisms
! method below):
* ((<URL:http://www.genome.jp/kegg/catalog/org_list.html>))
***************
*** 623,627 ****
# * get_similarity_between_genes
! This problem is fixed in the version 3.2.
+ ArrayOfSSDBRelation
--- 629,633 ----
# * get_similarity_between_genes
! This problem is fixed in the KEGG API version 3.2.
+ ArrayOfSSDBRelation
***************
*** 672,675 ****
--- 678,695 ----
ArrayOfLinkDBRelation data type is a list of the LinkDBRelation data type.
+ + PathwayElement
+
+ PathwayElement data type contains the following fields:
+
+ element_id unique identifier of the object on the pathway (int)
+ type type of the object ("gene", "enzyme" etc.) (string)
+ names array of names of the object (ArrayOfstring)
+ components array of element_ids of the group components (ArrayOfint)
+
+ + ArrayOfPathwayElement
+
+ ArrayOfPathwayElement data type is a list of the PathwayElement data type.
+
+
=== Methods
***************
*** 770,773 ****
--- 790,806 ----
btit("hsa:1798 mmu:13478 dme:CG5287-PA cel:Y60A3A.14")
+ --- bconv(string)
+
+ The bconv command converts external IDs (NCBI GI, NCBI GeneID, GenBank ID,
+ and UniProt ID) to KEGG IDs. The result is the tab separated pair of the
+ given ID and the converted ID in each line.
+
+ Return value:
+ string
+
+ Example:
+ # Convert NCBI GI and NCBI GeneID to KEGG genes_id
+ serv.bconv("ncbi-gi:10047086 ncbi-gi:10047090 ncbi-geneid:14751")
+
==== LinkDB
***************
*** 785,788 ****
--- 818,970 ----
get_linkdb_by_entry('eco:b0002', 'pathway', 11, 10)
+ + Relation among genes and enzymes
+
+ --- get_genes_by_enzyme(enzyme_id, org)
+
+ Retrieve all genes of the given organism.
+
+ Return value:
+ ArrayOfstring (genes_id)
+
+ Example:
+ # Returns all the GENES entry IDs in E.coli genome which are assigned
+ # EC number ec:1.2.1.1
+ get_genes_by_enzyme('ec:1.2.1.1', 'eco')
+
+ --- get_enzymes_by_gene(genes_id)
+
+ Retrieve all the EC numbers which are assigned to the given gene.
+
+ Return value:
+ ArrayOfstring (enzyme_id)
+
+ Example:
+ # Returns the EC numbers which are assigned to E.coli genes b0002
+ get_enzymes_by_gene('eco:b0002')
+
+
+ + Relation among enzymes, compounds and reactions
+
+ --- get_enzymes_by_compound(compound_id)
+
+ Retrieve all enzymes which have a link to the given compound_id.
+
+ Return value:
+ ArrayOfstring (enzyme_id)
+
+ Example:
+ # Returns the ENZYME entry IDs which have a link to the COMPOUND entry,
+ # 'cpd:C00345'
+ get_enzymes_by_compound('cpd:C00345')
+
+ --- get_enzymes_by_glycan(glycan_id)
+
+ Retrieve all enzymes which have a link to the given glycan_id.
+
+ Return value:
+ ArrayOfstring (enzyme_id)
+
+ Example
+ # Returns the ENZYME entry IDs which have a link to the GLYCAN entry,
+ # 'gl:G00001'
+ get_enzymes_by_glycan('gl:G00001')
+
+ --- get_enzymes_by_reaction(reaction_id)
+
+ Retrieve all enzymes which have a link to the given reaction_id.
+
+ Return value:
+ ArrayOfstring (enzyme_id)
+
+ Example:
+ # Returns the ENZYME entry IDs which have a link to the REACTION entry,
+ # 'rn:R00100'.
+ get_enzymes_by_reaction('rn:R00100')
+
+ --- get_compounds_by_enzyme(enzyme_id)
+
+ Retrieve all compounds which have a link to the given enzyme_id.
+
+ Return value:
+ ArrayOfstring (compound_id)
+
+ Example:
+ # Returns the COMPOUND entry IDs which have a link to the ENZYME entry,
+ # 'ec:2.7.1.12'.
+ get_compounds_by_enzyme('ec:2.7.1.12')
+
+ --- get_compounds_by_reaction(reaction_id)
+
+ Retrieve all compounds which have a link to the given reaction_id.
+
+ Return value:
+ ArrayOfstring (compound_id)
+
+ Example:
+ # Returns the COMPOUND entry IDs which have a link to the REACTION entry,
+ # 'rn:R00100'
+ get_compounds_by_reaction('rn:R00100')
+
+ --- get_glycans_by_enzyme(enzyme_id)
+
+ Retrieve all glycans which have a link to the given enzyme_id.
+
+ Return value:
+ ArrayOfstring (glycan_id)
+
+ Example
+ # Returns the GLYCAN entry IDs which have a link to the ENZYME entry,
+ # 'ec:2.4.1.141'
+ get_glycans_by_enzyme('ec:2.4.1.141')
+
+ --- get_glycans_by_reaction(reaction_id)
+
+ Retrieve all glycans which have a link to the given reaction_id.
+
+ Return value:
+ ArrayOfstring (glycan_id)
+
+ Example
+ # Returns the GLYCAN entry IDs which have a link to the REACTION entry,
+ # 'rn:R06164'
+ get_glycans_by_reaction('rn:R06164')
+
+ --- get_reactions_by_enzyme(enzyme_id)
+
+ Retrieve all reactions which have a link to the given enzyme_id.
+
+ Return value:
+ ArrayOfstring (reaction_id)
+
+ Example:
+ # Returns the REACTION entry IDs which have a link to the ENZYME entry,
+ # 'ec:2.7.1.12'
+ get_reactions_by_enzyme('ec:2.7.1.12')
+
+ --- get_reactions_by_compound(compound_id)
+
+ Retrieve all reactions which have a link to the given compound_id.
+
+ Return value:
+ ArrayOfstring (reaction_id)
+
+ Example:
+ # Returns the REACTION entry IDs which have a link to the COMPOUND entry,
+ # 'cpd:C00199'
+ get_reactions_by_compound('cpd:C00199')
+
+ --- get_reactions_by_glycan(glycan_id)
+
+ Retrieve all reactions which have a link to the given glycan_id.
+
+ Return value:
+ ArrayOfstring (reaction_id)
+
+ Example
+ # Returns the REACTION entry IDs which have a link to the GLYCAN entry,
+ # 'gl:G00001'
+ get_reactions_by_glycan('gl:G00001')
+
+
==== SSDB
***************
*** 1031,1034 ****
--- 1213,1252 ----
color_pathway_by_objects('path:eco00260', obj_list, fg_list, bg_list)
+ --- color_pathway_by_elements(pathway_id, element_id_list, fg_color_list, bg_color_list)
+
+ Color the objects (rectangles and circles on a pathway map) corresponding
+ to the given 'element_id_list' with the specified colors and return the
+ URL of the colored image. 'fg_color_list' is used for specifying the
+ color of text and border of the objects with given 'element_id_list' and
+ 'bg_color_list' is used for its background area. The order of colors in
+ these lists correspond with the order of objects in the 'element_id_list'
+ list.
+
+ This method is useful to specify which graphical object on the pathway
+ to be colored as there are some cases that multiple genes are assigned to
+ one rectangle or a gene is assigned to more than one rectangle on the
+ pathway map. The 'element_id' is an unique numerical identifier on the
+ pathway defined by the KGML (XML represeentation of the KEGG PATHWAY)
+ in the <entry> tag. List of the 'element_id's can be obtained by the
+ 'get_elements_by_pathway' method.
+
+ For more details on KGML, see:
+
+ * ((<URL:http://www.genome.jp/kegg/xml/>))
+
+ Return value:
+ string (URL)
+
+ Example:
+ # Returns the URL of the colored image of given pathway 'path:bsu00010' with
+ # * gene bsu:BG11350 (element_id 78, ec:3.2.1.86) colored in red on yellow
+ # * gene bsu:BG11203 (element_id 79, ec:3.2.1.86) colored in blue on yellow
+ # * gene bsu:BG11685 (element_id 51, ec:2.7.1.2) colored in red on orange
+ # * gene bsu:BG11685 (element_id 47, ec:2.7.1.2) colored in blue on orange
+ element_id_list = [ 78, 79, 51, 47 ]
+ fg_list = [ '#ff0000', '#0000ff', '#ff0000', '#0000ff' ]
+ bg_list = [ '#ffff00', '#ffff00', '#ffcc00', '#ffcc00' ]
+ color_pathway_by_elements('path:bsu00010', element_id_list, fg_list, bg_list)
+
--- get_html_of_marked_pathway_by_objects(pathway_id, object_id_list)
***************
*** 1060,1066 ****
Example:
# Returns the URL of the HTML which can be passed to the web browser
! # as a clickable map of coloerd image of the given pathway 'path:eco00970'
# with a gene 'eco:b4258' colored in gray/red, a compound 'cpd:C00135'
! # coloerd in green/yellow and a KO 'ko:K01881' colored in blue/orange.
obj_list = ['eco:b4258', 'cpd:C00135', 'ko:K01881']
fg_list = ['gray', '#00ff00', 'blue']
--- 1278,1284 ----
Example:
# Returns the URL of the HTML which can be passed to the web browser
! # as a clickable map of colored image of the given pathway 'path:eco00970'
# with a gene 'eco:b4258' colored in gray/red, a compound 'cpd:C00135'
! # colored in green/yellow and a KO 'ko:K01881' colored in blue/orange.
obj_list = ['eco:b4258', 'cpd:C00135', 'ko:K01881']
fg_list = ['gray', '#00ff00', 'blue']
***************
*** 1068,1074 ****
--- 1286,1338 ----
get_html_of_colored_pathway_by_objects('path:eco00970', obj_list, fg_list, bg_list)
+ --- get_html_of_colored_pathway_by_elements(pathway_id, element_id_list, fg_color_list, bg_color_list)
+
+ HTML version of the 'color_pathway_by_elements' method.
+ Color the objects corresponding to the given 'element_id_list' on the pathway
+ map with the specified colors and return the URL of the HTML containing the
+ colored image as a clickable map.
+
+ Return value:
+ string (URL)
+
+ Example:
+ # Returns the URL of the HTML which can be passed to the web browser as a
+ # clickable map of colored image of the given pathway 'path:bsu00010' with
+ # * gene bsu:BG11350 (element_id 78, ec:3.2.1.86) colored in red on yellow
+ # * gene bsu:BG11203 (element_id 79, ec:3.2.1.86) colored in blue on yellow
+ # * gene bsu:BG11685 (element_id 51, ec:2.7.1.2) colored in red on orange
+ # * gene bsu:BG11685 (element_id 47, ec:2.7.1.2) colored in blue on orange
+ element_id_list = [ 78, 79, 51, 47 ]
+ fg_list = [ '#ff0000', '#0000ff', '#ff0000', '#0000ff' ]
+ bg_list = [ '#ffff00', '#ffff00', '#ffcc00', '#ffcc00' ]
+ get_html_of_colored_pathway_by_elements('path:bsu00010', element_id_list, fg_list, bg_list)
+ Objects on the pathway
+ --- get_elements_by_pathway(pathway_id)
+
+ Search all objects on the specified pathway. This method will be used in
+ combination with the color_pathway_by_elements method to distingish graphical
+ objects on the pathway sharing the same name.
+
+ Return value:
+ ArrayOfPathwayElement
+
+ Example:
+ # Returns list of PathwayElement on the pathway map 'path:bsu00010'
+ get_elements_by_pathway('path:bsu00010')
+
+ # Find entry_ids for genes 'bsu:BG11350', 'bsu:BG11203' and 'bsu:BG11685'
+ # in Ruby language
+ elems = serv.get_elements_by_pathway('path:bsu00010')
+ genes = [ 'bsu:BG11350', 'bsu:BG11203', 'bsu:BG11685' ]
+ elems.each do |elem|
+ genes.each do |gene|
+ if elem.names.include?(gene)
+ puts gene, elem.element_id
+ end
+ end
+ end
+
--- get_genes_by_pathway(pathway_id)
***************
*** 1227,1379 ****
- + Relation among genes and enzymes
-
- --- get_genes_by_enzyme(enzyme_id, org)
-
- Retrieve all genes of the given organism.
-
- Return value:
- ArrayOfstring (genes_id)
-
- Example:
- # Returns all the GENES entry IDs in E.coli genome which are assigned
- # EC number ec:1.2.1.1
- get_genes_by_enzyme('ec:1.2.1.1', 'eco')
-
- --- get_enzymes_by_gene(genes_id)
-
- Retrieve all the EC numbers which are assigned to the given gene.
-
- Return value:
- ArrayOfstring (enzyme_id)
-
- Example:
- # Returns the EC numbers which are assigned to E.coli genes b0002
- get_enzymes_by_gene('eco:b0002')
-
-
- + Relation among enzymes, compounds and reactions
-
- --- get_enzymes_by_compound(compound_id)
-
- Retrieve all enzymes which have a link to the given compound_id.
-
- Return value:
- ArrayOfstring (enzyme_id)
-
- Example:
- # Returns the ENZYME entry IDs which have a link to the COMPOUND entry,
- # 'cpd:C00345'
- get_enzymes_by_compound('cpd:C00345')
-
- --- get_enzymes_by_glycan(glycan_id)
-
- Retrieve all enzymes which have a link to the given glycan_id.
-
- Return value:
- ArrayOfstring (enzyme_id)
-
- Example
- # Returns the ENZYME entry IDs which have a link to the GLYCAN entry,
- # 'gl:G00001'
- get_enzymes_by_glycan('gl:G00001')
-
- --- get_enzymes_by_reaction(reaction_id)
-
- Retrieve all enzymes which have a link to the given reaction_id.
-
- Return value:
- ArrayOfstring (enzyme_id)
-
- Example:
- # Returns the ENZYME entry IDs which have a link to the REACTION entry,
- # 'rn:R00100'.
- get_enzymes_by_reaction('rn:R00100')
-
- --- get_compounds_by_enzyme(enzyme_id)
-
- Retrieve all compounds which have a link to the given enzyme_id.
-
- Return value:
- ArrayOfstring (compound_id)
-
- Example:
- # Returns the COMPOUND entry IDs which have a link to the ENZYME entry,
- # 'ec:2.7.1.12'.
- get_compounds_by_enzyme('ec:2.7.1.12')
-
- --- get_compounds_by_reaction(reaction_id)
-
- Retrieve all compounds which have a link to the given reaction_id.
-
- Return value:
- ArrayOfstring (compound_id)
-
- Example:
- # Returns the COMPOUND entry IDs which have a link to the REACTION entry,
- # 'rn:R00100'
- get_compounds_by_reaction('rn:R00100')
-
- --- get_glycans_by_enzyme(enzyme_id)
-
- Retrieve all glycans which have a link to the given enzyme_id.
-
- Return value:
- ArrayOfstring (glycan_id)
-
- Example
- # Returns the GLYCAN entry IDs which have a link to the ENZYME entry,
- # 'ec:2.4.1.141'
- get_glycans_by_enzyme('ec:2.4.1.141')
-
- --- get_glycans_by_reaction(reaction_id)
-
- Retrieve all glycans which have a link to the given reaction_id.
-
- Return value:
- ArrayOfstring (glycan_id)
-
- Example
- # Returns the GLYCAN entry IDs which have a link to the REACTION entry,
- # 'rn:R06164'
- get_glycans_by_reaction('rn:R06164')
-
- --- get_reactions_by_enzyme(enzyme_id)
-
- Retrieve all reactions which have a link to the given enzyme_id.
-
- Return value:
- ArrayOfstring (reaction_id)
-
- Example:
- # Returns the REACTION entry IDs which have a link to the ENZYME entry,
- # 'ec:2.7.1.12'
- get_reactions_by_enzyme('ec:2.7.1.12')
-
- --- get_reactions_by_compound(compound_id)
-
- Retrieve all reactions which have a link to the given compound_id.
-
- Return value:
- ArrayOfstring (reaction_id)
-
- Example:
- # Returns the REACTION entry IDs which have a link to the COMPOUND entry,
- # 'cpd:C00199'
- get_reactions_by_compound('cpd:C00199')
-
- --- get_reactions_by_glycan(glycan_id)
-
- Retrieve all reactions which have a link to the given glycan_id.
-
- Return value:
- ArrayOfstring (reaction_id)
-
- Example
- # Returns the REACTION entry IDs which have a link to the GLYCAN entry,
- # 'gl:G00001'
- get_reactions_by_glycan('gl:G00001')
-
-
==== GENES
--- 1491,1494 ----
***************
*** 1432,1436 ****
== Notes
! Last updated: May 31, 2005
=end
--- 1547,1551 ----
== Notes
! Last updated: Feb 17, 2006
=end
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