Get_Pathway_Genes_by_Entrez_gene_identrez_gene_id00 Give an entrez gene id 2012-03-27 14:47:33.394 CEST 3064 2012-03-02 17:53:56.284 CET fg_color00 Foreground color for the image object 2012-04-14 16:51:17.489 CEST blue orange 2012-04-14 16:53:30.479 CEST bg_color00 red orange 2012-04-14 16:53:45.341 CEST Background color for the image object 2012-04-14 16:51:31.709 CEST Pathway Pathways associated to our input gene id 2012-04-14 16:52:13.836 CEST geneList Genes associated to the pathway output 2012-04-14 16:52:39.665 CEST url url of the colored image 2012-04-14 16:51:59.377 CEST image Pathway image 2012-04-14 16:51:41.10 CEST get_pathways_by_genesgenes_id_list1return11net.sf.taverna.t2.activitieswsdl-activity1.3net.sf.taverna.t2.activities.wsdl.WSDLActivity http://soap.genome.jp/KEGG.wsdl get_pathways_by_genes net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeget_genes_by_pathwaypathway_id0return11net.sf.taverna.t2.activitieswsdl-activity1.3net.sf.taverna.t2.activities.wsdl.WSDLActivity http://soap.genome.jp/KEGG.wsdl get_genes_by_pathway net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetPathwayDescriptionstring0return00net.sf.taverna.t2.activitieswsdl-activity1.3net.sf.taverna.t2.activities.wsdl.WSDLActivity http://soap.genome.jp/KEGG.wsdl btit net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeadd_ncbi_to_stringinput0output00net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity input 0 'text/plain' java.lang.String true output 0 'text/plain' 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeconvertToKEGGidstring0return00net.sf.taverna.t2.activitieswsdl-activity1.3net.sf.taverna.t2.activities.wsdl.WSDLActivity http://soap.genome.jp/KEGG.wsdl bconv net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesplitAndSendOnlyKEGGgeneIDstring0regex0split11net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity string 0 'text/plain' java.lang.String true regex 0 'text/plain' java.lang.String true split 1 1 workflow org.embl.ebi.escience.scuflworkers.java.SplitByRegex UserNameHere 2011-10-07 10:20:21.64 CEST net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokelisterstring0regex0split11net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity string 0 'text/plain' java.lang.String true regex 0 'text/plain' java.lang.String true split 1 1 workflow org.embl.ebi.escience.scuflworkers.java.SplitByRegex UserNameHere 2011-10-07 10:13:12.992 CEST net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesplitOnTabvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity \t net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSplitOnNewLinevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity \n net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeClean_List_of_Strings_by_separatorstringlist1separators0filteredlist11net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true separators 0 'text/plain' java.lang.String true filteredlist 1 1 workflow org.embl.ebi.escience.scuflworkers.java.FilterStringList UserNameHere 2012-03-08 10:58:28.266 CET net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeseparators_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity [:] net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokecolor_pathway_by_objectsobject_id_list1fg_color_list1bg_color_list1pathway_id0return00net.sf.taverna.t2.activitieswsdl-activity1.3net.sf.taverna.t2.activities.wsdl.WSDLActivity http://soap.genome.jp/KEGG.wsdl color_pathway_by_objects net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGet_image_from_URLurl0image00net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity url 0 'text/x-taverna-web-url' java.lang.String true base 0 'text/x-taverna-web-url' java.lang.String true image 0 'image/*' 0 workflow org.embl.ebi.escience.scuflworkers.java.WebImageFetcher net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeget_pathways_by_genesgenes_id_listlistersplitget_genes_by_pathwaypathway_idget_pathways_by_genesreturngetPathwayDescriptionstringget_pathways_by_genesreturnadd_ncbi_to_stringinputentrez_gene_idconvertToKEGGidstringadd_ncbi_to_stringoutputsplitAndSendOnlyKEGGgeneIDstringconvertToKEGGidreturnsplitAndSendOnlyKEGGgeneIDregexsplitOnTabvaluelisterstringsplitAndSendOnlyKEGGgeneIDsplitlisterregexSplitOnNewLinevalueClean_List_of_Strings_by_separatorstringlistget_genes_by_pathwayreturnClean_List_of_Strings_by_separatorseparatorsseparators_valuevaluecolor_pathway_by_objectsobject_id_listget_genes_by_pathwayreturncolor_pathway_by_objectsfg_color_listfg_colorcolor_pathway_by_objectsbg_color_listbg_colorcolor_pathway_by_objectspathway_idget_pathways_by_genesreturnGet_image_from_URLurlcolor_pathway_by_objectsreturnPathwaygetPathwayDescriptionreturngeneListClean_List_of_Strings_by_separatorfilteredlisturlcolor_pathway_by_objectsreturnimageGet_image_from_URLimage 7ad9cb44-4b8e-4bdf-afce-34de578afa7f 2011-10-07 10:18:35.742 CEST 64861873-b92f-4937-b693-d9368ac1bd84 2011-10-12 11:49:51.827 CEST 4b2f9602-ed5c-4f7a-858b-719f4373638c 2012-03-27 14:47:53.901 CEST 4fdff770-5e4f-40be-bd49-37a163b7663a 2011-10-06 16:38:57.134 CEST Eleni Mina 2012-03-27 14:49:09.456 CEST 763e457e-70f5-46a7-859c-c4b9d59bc67f 2011-10-06 16:42:11.693 CEST 05fbe49f-cde6-446b-ac11-af7cec97ee64 2012-03-07 17:09:55.351 CET b2303a05-1c33-4136-b44a-ae035f350bb3 2011-10-06 16:35:45.237 CEST 71b553ba-a4d0-4689-86d4-530e88aac7a9 2011-10-24 10:19:26.177 CEST a9655187-6bc6-46c8-84f6-78440a54a6b4 2012-04-14 16:52:37.292 CEST d7daee5a-e359-4999-95c9-45059158f5aa 2011-10-05 15:32:08.843 CEST 490b9fc3-4ec2-4816-8f5f-94874dd78e0d 2011-10-06 17:02:53.374 CEST 13e12c2a-0ee9-4044-9f05-da96e0d2a0ee 2011-10-07 10:25:33.702 CEST 7848b3af-653b-4f67-a7a4-0ba72766f3b8 2011-10-07 11:41:10.870 CEST ed2a5cf3-cea9-4da1-ad50-11892711059a 2012-04-13 21:42:51.677 CEST a0591b41-7527-4520-a183-54b704d3678f 2011-10-06 16:47:10.13 CEST 235a7eb9-4e5e-450a-abe5-a918d846ba55 2011-10-06 16:32:35.997 CEST 063d8eb3-fa2e-45c7-8ce7-f4ce50b1171f 2011-10-06 16:45:02.263 CEST 56b90bd5-1cbb-41d9-a6b7-46c340cf96ec 2011-10-07 10:24:11.386 CEST 7149243d-38dd-402f-b247-9b0be7b35852 2012-04-14 16:59:41.297 CEST Get Pathway-Genes by Entrez gene id 2012-03-07 17:12:35.637 CET 32496531-2939-4356-bd5b-dcba601923ef 2011-10-05 15:31:06.429 CEST ea8ebcb7-0f6d-47a6-a8bf-77129dada441 2012-03-07 16:59:03.836 CET d03e9678-1b49-4d2e-b00f-7501f4e49938 2011-10-06 16:42:58.554 CEST 910077fd-a6ec-4443-8e12-dea5e558b58a 2011-10-06 17:22:23.977 CEST c706c0fb-23d3-4905-a843-c8b1393df65a 2012-03-08 10:58:45.83 CET f47d95f1-35f3-4924-baa1-020b4f04f425 2012-04-14 16:51:27.842 CEST ceac8be0-f3f7-4c35-8af1-1cdfc12b800c 2011-10-06 17:01:40.102 CEST 15b2bf6b-7c2c-4f51-a359-e71311c38f0c 2011-10-06 16:23:58.454 CEST 6872a2c6-e45b-4b72-816f-1c15643da52c 2012-03-08 12:34:44.427 CET dbd70e63-4451-42c1-b7af-1797ed0b921b 2012-04-14 16:54:06.358 CEST 64fcc31e-a543-4987-9b88-b9be856bedbe 2011-10-06 16:49:24.958 CEST 7b2ca01a-7c41-42b9-ae70-5e54793ef46c 2011-10-24 10:17:52.737 CEST d536500c-2b90-454e-91db-e4dd2d2c2a8b 2011-10-07 10:36:58.473 CEST 231c2709-43cd-4fc5-85bd-9468f1eea95a 2012-04-13 21:50:41.249 CEST Given a specific entrez gene id, returns the pathways that this gene participates in and for each of those pathways which genes are associated with. The workflow outputs also a KEGG pathway map and the objects are colored according to the input color values. 2012-04-14 16:58:24.961 CEST c0163a24-aa81-419a-9ef6-9e08199b6087 2012-03-27 14:49:18.61 CEST 6c3ced8e-4893-46f9-aa79-6bdd6727136e 2012-03-27 15:05:46.613 CEST 82304800-d0da-4039-867f-da1f6d2aec43 2012-04-14 16:53:27.459 CEST c0163a24-aa81-419a-9ef6-9e08199b6087 2012-03-27 15:09:18.109 CEST dc5c8494-d5ad-4d1c-ae59-b6446e332ff6 2012-04-14 16:52:12.275 CEST 7326dc17-e3cb-4e55-abf4-9ac9865b8195 2011-10-07 10:22:07.870 CEST cef714db-7546-48ea-b513-3c0c7e34da64 2011-10-06 16:00:59.839 CEST bc443350-7b01-4519-8ea5-0860116dbfdd 2012-03-27 14:46:42.903 CEST ad02e084-2b2d-4b7d-8a7f-d835eeb7b9d6 2012-04-14 16:51:58.115 CEST 5361d91f-b2e3-41d5-85f2-fbc94b64afa3 2012-03-27 12:46:22.131 CEST 80f388e0-6b2c-4279-962d-fa5377a2fd07 2011-10-06 15:46:55.78 CEST 7b86438c-fa16-4a98-97a5-d8193873bc35 2012-03-07 16:57:25.330 CET 69e26900-1320-407a-b6fc-6c856a2cf441 2012-04-13 21:44:03.366 CEST 4886aa26-cc6a-4cc7-b6ad-19b1fb08db76 2011-10-24 13:25:30.560 CEST 18821246-a3d7-4e4d-8842-fa86213a6f1c 2012-04-14 16:58:16.94 CEST 1addceb6-e32f-4b70-ad47-8bc47a28e429 2012-04-14 16:53:43.283 CEST 198a0f09-9230-4b38-a0a6-5c7244c18ac2 2012-03-07 17:13:56.356 CET bb020622-2a80-4888-bb2f-4a1a4d05eb1e 2011-10-07 10:13:24.590 CEST 67a3a39f-f4dc-457c-a463-e03ffa21daaa 2012-03-07 17:45:17.651 CET 6109021c-8ef5-4f48-92ca-886e30d4c4e7 2011-10-07 10:29:17.457 CEST 96684730-327f-41d2-b571-dbd1eed8d9b6 2011-10-07 10:20:31.990 CEST 22324a52-626c-448e-a6d8-7327abeb4c1e 2011-10-05 15:30:00.162 CEST 3c8eb060-a449-4283-a344-4e2585fcffdc 2011-10-06 16:39:51.453 CEST 99a4934b-56df-4cda-88d0-b1d47eac9604 2012-03-07 16:53:50.856 CET 6d0493ef-b040-4955-98b9-afe14cedb83a 2011-10-07 10:11:04.308 CEST d2c2663b-c89a-4957-84cb-b57147be5491 2012-03-02 18:24:29.193 CET 5949e616-fa4e-49c8-91e9-78291361db12 2012-03-07 17:12:38.546 CET