PW2ENSwp_id00 A WikiPathway identifier 2015-08-31 09:02:27.27 UTC WP176 2015-08-31 09:02:18.557 UTC ensembl_id_list ENSEMBL identifer 2015-08-31 11:14:21.607 UTC ENSG00000005381 2015-08-31 11:19:03.317 UTC getENSXrefList0responseBody00 The WikiPathways Webservice/API is queried for ENSEMBL identifiers in the given pathway. 2015-08-31 11:13:50.53 UTC net.sf.taverna.t2.activitiesrest-activity1.4net.sf.taverna.t2.activities.rest.RESTActivity GET http://webservice.wikipathways.org/getXrefList?pwId={}&code=En application/xml application/xml String false false false false true java.lang.String net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeParse_ens_idxml_text0nodelist11 The ENSEMBL identifiers are parsed from the WikiPathways XML file output. 2015-08-31 11:14:05.53 UTC net.sf.taverna.t2.activitiesxpath-activity1.4net.sf.taverna.t2.activities.xpath.XPathActivity <?xml version="1.0" encoding="UTF-8"?> <ns1:getXrefListResponse xmlns:ns1="http://www.wso2.org/php/xsd" xmlns:ns2="http://www.wikipathways.org/webservice"> <ns1:xrefs>15372</ns1:xrefs> <ns1:xrefs>15377</ns1:xrefs> <ns1:xrefs>15379</ns1:xrefs> <ns1:xrefs>15414</ns1:xrefs> <ns1:xrefs>15422</ns1:xrefs> <ns1:xrefs>15428</ns1:xrefs> <ns1:xrefs>15544</ns1:xrefs> <ns1:xrefs>15553</ns1:xrefs> <ns1:xrefs>15627</ns1:xrefs> <ns1:xrefs>15636</ns1:xrefs> <ns1:xrefs>15641</ns1:xrefs> <ns1:xrefs>16238</ns1:xrefs> <ns1:xrefs>16240</ns1:xrefs> <ns1:xrefs>16467</ns1:xrefs> <ns1:xrefs>16474</ns1:xrefs> <ns1:xrefs>16480</ns1:xrefs> <ns1:xrefs>16643</ns1:xrefs> <ns1:xrefs>16761</ns1:xrefs> <ns1:xrefs>17015</ns1:xrefs> <ns1:xrefs>17115</ns1:xrefs> <ns1:xrefs>17230</ns1:xrefs> <ns1:xrefs>17482</ns1:xrefs> <ns1:xrefs>17561</ns1:xrefs> <ns1:xrefs>17621</ns1:xrefs> <ns1:xrefs>17627</ns1:xrefs> <ns1:xrefs>17855</ns1:xrefs> <ns1:xrefs>18009</ns1:xrefs> <ns1:xrefs>18272</ns1:xrefs> <ns1:xrefs>18349</ns1:xrefs> <ns1:xrefs>18405</ns1:xrefs> <ns1:xrefs>18420</ns1:xrefs> <ns1:xrefs>18421</ns1:xrefs> <ns1:xrefs>20506</ns1:xrefs> <ns1:xrefs>209153</ns1:xrefs> <ns1:xrefs>24103</ns1:xrefs> <ns1:xrefs>25567</ns1:xrefs> <ns1:xrefs>25812</ns1:xrefs> <ns1:xrefs>25941</ns1:xrefs> <ns1:xrefs>27470</ns1:xrefs> <ns1:xrefs>28728</ns1:xrefs> <ns1:xrefs>29033</ns1:xrefs> <ns1:xrefs>29035</ns1:xrefs> <ns1:xrefs>29105</ns1:xrefs> <ns1:xrefs>29222</ns1:xrefs> <ns1:xrefs>29311</ns1:xrefs> <ns1:xrefs>33101</ns1:xrefs> <ns1:xrefs>37445</ns1:xrefs> <ns1:xrefs>39025</ns1:xrefs> <ns1:xrefs>39026</ns1:xrefs> <ns1:xrefs>39027</ns1:xrefs> <ns1:xrefs>44454</ns1:xrefs> <ns1:xrefs>47775</ns1:xrefs> <ns1:xrefs>47776</ns1:xrefs> <ns1:xrefs>CHEBI:15372</ns1:xrefs> <ns1:xrefs>CHEBI:15377</ns1:xrefs> <ns1:xrefs>CHEBI:15379</ns1:xrefs> <ns1:xrefs>CHEBI:15414</ns1:xrefs> <ns1:xrefs>CHEBI:15422</ns1:xrefs> <ns1:xrefs>CHEBI:15428</ns1:xrefs> <ns1:xrefs>CHEBI:15544</ns1:xrefs> <ns1:xrefs>CHEBI:15553</ns1:xrefs> <ns1:xrefs>CHEBI:15627</ns1:xrefs> <ns1:xrefs>CHEBI:15636</ns1:xrefs> <ns1:xrefs>CHEBI:15641</ns1:xrefs> <ns1:xrefs>CHEBI:16238</ns1:xrefs> <ns1:xrefs>CHEBI:16240</ns1:xrefs> <ns1:xrefs>CHEBI:16467</ns1:xrefs> <ns1:xrefs>CHEBI:16474</ns1:xrefs> <ns1:xrefs>CHEBI:16480</ns1:xrefs> <ns1:xrefs>CHEBI:16643</ns1:xrefs> <ns1:xrefs>CHEBI:16761</ns1:xrefs> <ns1:xrefs>CHEBI:17015</ns1:xrefs> <ns1:xrefs>CHEBI:17115</ns1:xrefs> <ns1:xrefs>CHEBI:17230</ns1:xrefs> <ns1:xrefs>CHEBI:17482</ns1:xrefs> <ns1:xrefs>CHEBI:17561</ns1:xrefs> <ns1:xrefs>CHEBI:17621</ns1:xrefs> <ns1:xrefs>CHEBI:17627</ns1:xrefs> <ns1:xrefs>CHEBI:18009</ns1:xrefs> <ns1:xrefs>CHEBI:18349</ns1:xrefs> <ns1:xrefs>CHEBI:18405</ns1:xrefs> <ns1:xrefs>CHEBI:18420</ns1:xrefs> <ns1:xrefs>CHEBI:18421</ns1:xrefs> <ns1:xrefs>CHEBI:20506</ns1:xrefs> <ns1:xrefs>CHEBI:209153</ns1:xrefs> <ns1:xrefs>CHEBI:24103</ns1:xrefs> <ns1:xrefs>CHEBI:25812</ns1:xrefs> <ns1:xrefs>CHEBI:25941</ns1:xrefs> <ns1:xrefs>CHEBI:27470</ns1:xrefs> <ns1:xrefs>CHEBI:28728</ns1:xrefs> <ns1:xrefs>CHEBI:29033</ns1:xrefs> <ns1:xrefs>CHEBI:29035</ns1:xrefs> <ns1:xrefs>CHEBI:29105</ns1:xrefs> <ns1:xrefs>CHEBI:29222</ns1:xrefs> <ns1:xrefs>CHEBI:29311</ns1:xrefs> <ns1:xrefs>CHEBI:44454</ns1:xrefs> <ns1:xrefs>CHEBI:62764</ns1:xrefs> </ns1:getXrefListResponse> /ns1:getXrefListResponse/ns1:xrefs ns2 http://www.wikipathways.org/webservice ns1 http://www.wso2.org/php/xsd net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSplit_string_into_string_list_by_regular_expressionregex0string0split11 Splits the input text on the newline (\n) character. 2015-08-31 12:30:28.215 UTC net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity string 0 'text/plain' java.lang.String true regex 0 'text/plain' java.lang.String true split 1 l('text/plain') 1 workflow org.embl.ebi.escience.scuflworkers.java.SplitByRegex net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregex_valuevalue00 Value for splitting the input text, in this case the newline (\n) character. 2015-08-31 12:31:00.365 UTC net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity \n net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_Listinputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity inputlist 2 l(l('')) [B true outputlist 1 l('') 1 workflow org.embl.ebi.escience.scuflworkers.java.FlattenList net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeMerge_String_List_to_a_String_2stringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true seperator 0 'text/plain' java.lang.String true concatenated 0 'text/plain' 0 workflow org.embl.ebi.escience.scuflworkers.java.StringListMerge net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetENSXrefListSplit_string_into_string_list_by_regular_expressionsplitParse_ens_idxml_textgetENSXrefListresponseBodySplit_string_into_string_list_by_regular_expressionregexregex_valuevalueSplit_string_into_string_list_by_regular_expressionstringwp_idFlatten_ListinputlistParse_ens_idnodelistMerge_String_List_to_a_String_2stringlistFlatten_Listoutputlistensembl_id_listMerge_String_List_to_a_String_2concatenated f9ec5b63-86f3-487e-b203-5b2b798e7718 2015-08-31 12:31:02.861 UTC 06b3da1f-c27b-4c0d-97f7-1a5b8d7121b7 2015-08-31 11:19:06.415 UTC Kristina Hettne 2015-08-31 11:02:33.4 UTC 9b9d915c-4194-47a6-8431-654e61cb68c6 2015-08-31 12:19:10.955 UTC e6ebf2cb-544d-45a1-8bb3-1916b2d7a5b3 2015-08-31 11:15:48.528 UTC 1bb35468-b509-4de2-acf0-0a8140e0b63b 2015-08-31 08:59:25.931 UTC 4bd2a71e-89b0-40e9-a303-27dda270885e 2015-08-31 09:02:33.789 UTC 2d670d51-1d96-4dd8-84e0-9ede6a50a339 2015-08-31 12:32:28.180 UTC 1cea5805-8808-4da8-a605-98b926244c56 2015-08-31 12:28:42.622 UTC 4f503713-57a1-40f4-b502-6d3a5bf02b0a 2015-08-31 11:07:42.264 UTC This workflow uses the WikiPathways Webservice/API to query to retrieve all ENSEMBL identifers for the given pathway. 2015-08-31 13:10:11.854 UTC 53339d3a-a905-40a7-b587-cbbb798cd9b9 2015-08-31 12:27:48.347 UTC 5001ed59-71dd-4a3f-879e-468c8b759acb 2015-08-31 11:13:13.392 UTC bb4ceaa9-d035-40e0-b95e-aec380120dc3 2015-08-31 13:09:17.422 UTC 13609497-fe10-458a-8081-103d635e35af 2015-08-31 13:10:13.742 UTC 1b57ab65-4a48-4ab2-9e9d-c942497cf621 2015-08-31 12:02:57.186 UTC 7c92f891-a19f-491d-b414-d8e6614ed824 2015-08-31 11:06:14.419 UTC PW2ENS 2015-08-31 13:08:52.534 UTC 08b780fc-8351-44fc-adf2-b71d33c63d9d 2015-10-08 11:18:05.521 UTC