AllPW2CHEBIwp_id00 A WikiPathway identifier 2015-08-31 09:02:27.27 UTC WP176 2015-08-31 09:02:18.557 UTC chebi_id_list1 Chemical Entities of Biological Interest (ChEBI) identifer 2015-08-31 11:07:27.162 UTC 15372 2015-08-31 11:07:39.761 UTC getChEBIXrefList0responseBody00 The WikiPathways Webservice/API is queried for Chemical Entities of Biological Interest (ChEBI) identifiers in the given pathway. 2015-08-31 11:05:17.438 UTC net.sf.taverna.t2.activitiesrest-activity1.5net.sf.taverna.t2.activities.rest.RESTActivity GET http://webservice.wikipathways.org/getXrefList?pwId={}&code=Ce application/xml application/xml String false false false false true java.lang.String net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeParse_chebi_idxml_text0nodelist11 The ChEBI identifiers are parsed from the WikiPathways XML file output. 2015-08-31 11:07:05.458 UTC net.sf.taverna.t2.activitiesxpath-activity1.5net.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-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSplit_string_into_string_list_by_regular_expressionregex0string0split11net.sf.taverna.t2.activitieslocalworker-activity1.5net.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-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregex_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.5net.sf.taverna.t2.activities.stringconstant.StringConstantActivity \n net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_Listinputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.5net.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-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRemove_String_Duplicatesstringlist1strippedlist11net.sf.taverna.t2.activitieslocalworker-activity1.5net.sf.taverna.t2.activities.localworker.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true strippedlist 1 l('text/plain') 1 workflow org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetChEBIXrefListSplit_string_into_string_list_by_regular_expressionsplitParse_chebi_idxml_textgetChEBIXrefListresponseBodySplit_string_into_string_list_by_regular_expressionregexregex_valuevalueSplit_string_into_string_list_by_regular_expressionstringwp_idFlatten_ListinputlistParse_chebi_idnodelistRemove_String_DuplicatesstringlistFlatten_Listoutputlistchebi_id_listRemove_String_Duplicatesstrippedlist 4bd2a71e-89b0-40e9-a303-27dda270885e 2015-08-31 09:02:33.789 UTC Kristina Hettne 2015-08-31 11:02:33.4 UTC 1bb35468-b509-4de2-acf0-0a8140e0b63b 2015-08-31 08:59:25.931 UTC AllPW2CHEBI 2015-08-31 13:08:00.558 UTC 738837df-5f02-4bdb-9577-8ec9e6f29a08 2015-08-31 12:25:54.473 UTC 15726c4d-95f3-429d-802e-521081364327 2015-08-31 12:03:35.667 UTC This workflow uses the WikiPathways Webservice/API to query to retrieve all Chemical Entities of Biological Interest (ChEBI) identifers for all pathways and merge them to one, unique list. 2015-08-31 13:09:55.54 UTC 7c92f891-a19f-491d-b414-d8e6614ed824 2015-08-31 11:06:14.419 UTC 4f503713-57a1-40f4-b502-6d3a5bf02b0a 2015-08-31 11:07:42.264 UTC e4ffd425-93d1-4ffe-b81c-5bc4a8ec6be7 2015-08-31 13:09:56.646 UTC a3b843a5-2260-4d6f-ae6a-98dfa9e1dc3b 2015-08-31 13:08:08.361 UTC