ADR_substantiationatc00 Workflow ATC input The 7 digit atc code of a drug 2011-02-08 18:29:15.460 CET M01AH01 2010-07-19 13:19:34.980 CEST The drug input. The ATC code of a drug (5th level, 7 digits) 2011-03-11 18:08:12.304 CET 2011-03-20 11:53:55.666 CET Workflow drug input The ACT code of a drug (5th level, 7 digits) 2011-03-11 17:43:54.128 CET Workflow ATC input 2010-07-19 13:19:29.11 CEST N05AD01 2011-03-20 11:54:15.83 CET event00 Workflow clinical event input Allowed events are: For the clinical events, the following input types are allowed: 1) UMLS CUI concept identifiers (single identifier or a list of identifiers) 2) clinical events observed as adverse drug reactions according to the EU-ADR project (see ref for details) 2011-03-11 17:47:43.212 CET 2011-03-20 12:41:32.610 CET The clinical event input For the clinical events, the following input types are allowed: 1) UMLS: UMLS CUI concept identifiers 2) EUADR_EVENT: clinical events observed as adverse drug reactions according to the EU-ADR project (see ref for details) If you use option 1), insert here a single UMLS CUI identifier or a list of identifiers. If you use option 2), insert here the name of the EUADR_EVENT as defined in ref. 2011-04-15 09:57:26.992 CEST Workflow clinical event input Allowed events are: For the clinical events, the following input types are allowed: 1) UMLS: UMLS CUI concept identifiers 2) EUADR_event: clinical events observed as adverse drug reactions according to the EU-ADR project (see ref for details) If you use option 1), insert here a single UMLS CUI identifier or a list of identifiers. If you use option 2), insert here the name of the EUADR_event as defined in ref. 2011-03-11 17:53:02.632 CET The clinical event input For the clinical events, the following input types are allowed: 1) UMLS: UMLS concept identifiers 2) EUADR_EVENT: clinical events observed as adverse drug reactions according to the EU-ADR project (see ref for details) If you use option 1), insert here a single UMLS concept identifier or a list of identifiers. If you use option 2), insert here the name of the EUADR_EVENT as defined in http://ibi.imim.es/ADR_Substantiation.html. 2011-07-29 15:57:36.998 CEST The clinical event input For the clinical events, the following input types are allowed: 1) UMLS: UMLS concept identifiers 2) EUADR_EVENT: clinical events observed as adverse drug reactions according to the EU-ADR project (see http://ibi.imim.es/ADR_Substantiation.html for details). If you use option 1), insert here a single UMLS concept identifier or a list of identifiers. If you use option 2), insert here the name of the EUADR_EVENT as defined in http://ibi.imim.es/ADR_Substantiation.html. 2011-07-29 16:38:28.536 CEST C0003811 C0023976 C0035828 C0040479 C1563715 2011-03-11 17:45:20.320 CET Workflow event input Allowed events are: 1) events of type EUADR_EVENT as defined in the EUADR project 2) events of type UMLS being a CUI concept identifier 2011-02-08 18:30:19.406 CET The clinical event input For the clinical events, the following input types are allowed: 1) UMLS: UMLS concept identifiers 2) EUADR_EVENT: clinical events observed as adverse drug reactions according to the EU-ADR project (see ref for details) If you use option 1), insert here a single UMLS concept identifier or a list of identifiers. If you use option 2), insert here the name of the EUADR_EVENT as defined in . 2011-07-29 15:56:51.84 CEST C0003811 C0023976 C0035828 C0040479 C1563715 C1832916 C1833154 C1835325 C1859062 C1859063 C1860467 C1863518 C1863519 C1867899 C1867904 C1970119 C2678483 C2678484 C2678485 2011-03-20 12:41:53.377 CET UGIB 2010-09-30 17:56:42.141 CEST Workflow clinical event input Allowed events are: 1) events of type EUADR_EVENT as defined in the EUADR project 2) events of type UMLS being a CUI concept identifier 2011-03-11 17:44:51.984 CET The clinical event input For the clinical events, the following input types are allowed: 1) UMLS: UMLS CUI concept identifiers 2) EUADR_event: clinical events observed as adverse drug reactions according to the EU-ADR project (see ref for details) If you use option 1), insert here a single UMLS CUI identifier or a list of identifiers. If you use option 2), insert here the name of the EUADR_event as defined in ref. 2011-03-11 18:08:40.212 CET 2011-02-08 18:29:52.77 CET Name of the event. This is only required for user-friendly visualization of the results. In particular, if the input is a CUI concept identifier. 2011-02-08 18:29:49.59 CET Workflow event input 2010-09-30 17:56:35.723 CEST 2011-03-11 17:44:58.278 CET eventType00 Type of the event to be processed. For the clinical events, the following types are allowed: 1) UMLS: if you use UMLS CUI concept identifiers (single identifier or a list of identifiers) 2) EUADR_EVENT: if you use clinical events as defined in the EU-ADR project 2011-04-15 09:56:27.129 CEST default = EUADR_EVENT 2011-02-08 18:30:38.742 CET EUADR_EVENT 2011-02-08 18:30:43.830 CET Type of the event to be processed. Must be either EUADR_EVENT if the event is defined in the EUADR project or UMLS if the event is a list of CUI concept identifiers 2011-02-08 18:30:37.869 CET Type of the event to be processed. Must be either EUADR_EVENT if the event is defined in the EUADR project or UMLS if the event is a list of CUI concept identifiers 2011-01-24 17:29:31.677 CET Type of the event to be processed. For the clinical events, the following types are allowed: 1) UMLS: if you use UMLS CUI concept identifiers (single identifier or a list of identifiers) 2) EUADR_event: if you use clinical events as defined in the EU-ADR project 2011-03-11 17:50:26.85 CET UMLS 2011-03-11 17:50:35.904 CET Type of the event to be processed. For the clinical events, the following types are allowed: 1) UMLS: if you use UMLS concept identifiers (single identifier or a list of identifiers) 2) EUADR_EVENT: if you use clinical events as defined in the EU-ADR project (see http://ibi.imim.es/ADR_Substantiation.html) 2011-07-29 15:58:38.772 CEST cytoscape00 Insert here the path to your local cytoscape installation. 2011-03-11 17:44:28.744 CET insert here the path to your local cytoscape installation e.g. /home/user/cytoscape-v2.7.0/ 2011-01-10 12:49:09.100 CET /home/user/cytoscape-v2.7.0 2011-01-10 12:46:23.859 CET cytoscape-v2.7.0 2011-01-10 12:46:17.448 CET insert here the path to your local cytoscape installation e.g. /home/user/cytoscape 2011-01-10 12:45:49.862 CET insert here the path to your local cytoscape installation e.g. /home/user/cytoscape-v2.7.0 2011-01-10 12:46:10.80 CET /home/user/Cytoscape_v2.7.0/ 2011-07-29 15:55:51.933 CEST Insert here the path to your local cytoscape installation e.g. /home/user/cytoscape-v2.7.0/ 2011-02-08 18:34:26.347 CET Insert here the path to your local Cytoscape installation. 2011-03-11 18:10:06.24 CET /home/user/cytoscape-v2.7.0/ 2011-01-10 12:49:14.15 CET eventName00 Acute liver injury 2011-03-11 17:54:30.364 CET Name of the event. This is only required for user-friendly visualization of the results. In particular, if the input is a CUI concept identifier. 2011-02-08 18:29:57.540 CET UGIB 2011-02-08 18:30:03.21 CET Long QT syndrome 2011-03-20 11:54:37.770 CET Define a name for the clinical event. This is required for user-friendly visualization of the results. 2011-07-29 15:58:01.879 CEST Define a name for the clinical event. This is only required for user-friendly visualization of the results. 2011-03-11 17:54:14.812 CET drugTargetsOutput Full XML output for the get drug targets web service. 2010-07-19 13:17:52.912 CEST Full XML output for the getDrugTargets web service. 2011-02-08 18:32:03.919 CET XML output file for the getDrugTargets web service. 2011-03-11 18:00:23.225 CET drugEventLinkingPathways List of biological pathways in which both proteins associated to the clinical event and to the drug are present. 2011-03-11 18:01:21.856 CET List of pathways in which at least one event and one drug protein are expressed. 2011-02-08 18:32:52.619 CET List of biological pathways that link the drug with the event. In each pathway contain proteins that are associated to the clinical event and to the drug. 2011-07-29 16:01:07.332 CEST eventProteinsOutput Full XML output for the get Disease Associated genes web service. 2010-07-19 13:19:17.699 CEST Full XML output for the getDiseaseAssociatedProteins web service. 2011-02-08 18:31:39.335 CET XML output file for the getDiseaseAssociatedProteins web service. 2011-03-11 18:00:03.328 CET drugEventLinkingProteins List of proteins that link the drug and the event. They represent the intersection between the Drug-Tarhresult from the intersection of the set of proteins annotated to the drug and the set of proteins annotated to the clinical event. 2011-07-29 16:02:08.860 CEST List of proteins annotated to both the clinical event and the drug. 2011-03-11 18:01:52.232 CET List of proteins annotated to both, event and drug. 2011-02-08 18:33:19.929 CET List of proteins that link the drug and the event. They represent the intersection between the Drug-Target-Profile and the Event-Protein-Profile. 2011-07-29 16:02:54.840 CEST List of proteins that result from the intersection of the set of proteins annotated to the drug and the set of proteins annotated to the clinical event. 2011-03-11 18:02:50.105 CET CytoscapeResultGraph Network file that can be visualized in Cytoscape. Simply save this file using the file extension .xgmml and open it in Cytoscape. It contains a multipartite graph in which the nodes are the drug, the clinical event and the proteins and the associations between them. 2011-07-29 15:59:11.272 CEST Network file that which can be visualized in Cytoscape. Simply store this file using the file extension .xgmml and open it in Cytoscape. It contains a multipartite graph in which the nodes are the drug, the clinical event and the proteins and the associations between them. 2011-03-11 17:58:45.680 CET Network file that which can be visualized in Cytoscape. Simply save this file using the file extension .xgmml and open it in Cytoscape. It contains a multipartite graph in which the nodes are the drug, the clinical event and the proteins and the associations between them. 2011-03-11 17:59:13.504 CET Cytoscape graph which can be openend in Cytoscape. Simply store this file using the file ending .xgmml and open it in Cytoscape. It contains the drug, event and their annotated proteins as well as supporting information such as link outs to publications etc. 2011-02-08 18:31:18.807 CET eventProteins List of proteins annotated to the clinical event. 2011-03-11 17:59:43.88 CET List of all proteins annoated to the event. 2011-02-08 18:31:29.111 CET drugTargets List of proteins annotated to the drug. 2011-02-08 18:31:51.496 CET CreateDiseaseProteinListstring0concatenated00fail00net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.StringListMerge workflow java.lang.String true string 0 l('text/plain') 0 concatenated 0 0 fail 0 UserNameHere 2011-01-27 12:48:28.442 CET UserNameHere 2011-01-27 12:54:47.847 CET UserNameHere 2011-01-27 12:58:24.852 CET UserNameHere 2011-01-27 14:01:57.290 CET UserNameHere 2011-01-27 12:48:44.599 CET UserNameHere 2011-03-16 11:53:10.628 CET UserNameHere 2011-02-10 11:26:20.837 CET UserNameHere 2011-02-10 11:14:16.435 CET UserNameHere 2011-03-16 12:43:37.265 CET UserNameHere 2011-03-16 12:34:50.409 CET net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegenerateProteinListseventProteins0drugProteins0output00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="proteinLists" name="proteinLists" qname="{http://service.adrPath.ibi.imim.es/xsd}proteinLists"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="eventProteins" qname="{http://service.adrPath.ibi.imim.es/xsd}&gt;proteinLists&gt;eventProteins" /><s:basetype optional="false" unbounded="false" typename="string" name="drugProteins" qname="{http://service.adrPath.ibi.imim.es/xsd}&gt;proteinLists&gt;drugProteins" /></s:elements></s:complextype></s:extensions> false eventProteins 0 'text/plain' false drugProteins 0 'text/plain' 0 output 0 'text/xml' net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeConvertToHTMLatc0intersectingPathways0event0EUADR_intersectingPathways00net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity net.sourceforge.taverna.scuflworkers.xml.XSLTWorker workflow java.lang.String true intersectingPathways 0 text/plain java.lang.String true atc 0 text/plain java.lang.String true event 0 text/plain 0 EUADR_intersectingPathways 0 UserNameHere 2011-02-08 14:46:35.637 CET UserNameHere 2011-01-10 14:35:06.569 CET UserNameHere 2011-01-04 17:28:55.745 CET UserNameHere 2011-01-07 11:05:44.551 CET UserNameHere 2011-01-07 13:02:47.919 CET UserNameHere 2011-01-24 14:12:31.876 CET UserNameHere 2011-01-07 13:13:55.151 CET UserNameHere 2011-01-07 11:00:56.265 CET UserNameHere 2011-01-07 17:01:44.948 CET UserNameHere 2011-01-07 10:59:55.696 CET UserNameHere 2011-01-07 11:04:06.140 CET UserNameHere 2011-01-07 17:03:53.968 CET UserNameHere 2011-01-07 15:28:56.549 CET UserNameHere 2011-01-04 17:35:25.767 CET UserNameHere 2011-02-11 17:38:06.464 CET UserNameHere 2011-01-07 13:00:00.84 CET UserNameHere 2011-03-16 13:02:19.820 CET UserNameHere 2011-03-16 12:50:45.227 CET UserNameHere 2011-02-08 14:40:17.130 CET UserNameHere 2011-01-07 11:06:39.488 CET UserNameHere 2011-02-11 17:30:33.232 CET UserNameHere 2011-04-15 13:31:55.549 CEST UserNameHere 2011-02-07 16:04:18.641 CET UserNameHere 2011-02-11 17:33:40.687 CET UserNameHere 2011-01-07 15:23:03.842 CET UserNameHere 2011-02-08 15:12:04.667 CET UserNameHere 2011-01-07 13:11:13.115 CET UserNameHere 2011-01-10 12:48:57.256 CET UserNameHere 2011-01-07 12:39:33.114 CET UserNameHere 2011-02-07 16:15:40.765 CET UserNameHere 2011-01-10 10:27:03.462 CET UserNameHere 2011-01-07 12:32:23.168 CET UserNameHere 2011-01-07 10:59:16.782 CET UserNameHere 2011-02-09 11:13:41.230 CET UserNameHere 2011-01-07 12:59:20.325 CET UserNameHere 2011-03-16 16:27:06.962 CET UserNameHere 2011-01-07 13:08:28.15 CET UserNameHere 2011-03-16 12:47:51.603 CET UserNameHere 2011-03-16 16:07:59.755 CET UserNameHere 2011-01-21 14:43:38.627 CET UserNameHere 2011-04-18 17:32:02.605 CEST UserNameHere 2011-02-11 17:24:18.555 CET UserNameHere 2011-01-07 13:11:29.19 CET UserNameHere 2011-01-24 14:12:54.675 CET UserNameHere 2011-01-10 12:42:11.271 CET UserNameHere 2011-01-07 15:19:59.88 CET UserNameHere 2011-02-11 17:28:36.0 CET UserNameHere 2011-01-04 17:41:26.968 CET UserNameHere 2011-01-04 17:42:55.522 CET UserNameHere 2011-01-07 13:15:44.385 CET UserNameHere 2011-01-07 12:35:20.444 CET UserNameHere 2011-02-11 17:25:04.791 CET net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeCheckConnectingPathwaysintersectionList1failDisease0failDrug0result00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true intersectionList 1 text/plain java.lang.String true failDisease 0 text/plain java.lang.String true failDrug 0 text/plain 0 result 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeXPath_getPathwaysxpath0xml-text0nodelist11net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker dom4j:dom4j:1.6 workflow dom4j dom4j 1.6 716010169 java.lang.String true xpath 0 'text/plain' java.lang.String true xml-text 0 'text/xml' 1 nodelist 1 l('text/plain') 1 nodelistAsXML 1 l('text/plain') net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokexpath_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.2net.sf.taverna.t2.activities.stringconstant.StringConstantActivity //ns3:pathway/ns3:name net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeTellResultmessage0net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity net.sourceforge.taverna.scuflworkers.ui.TellWorker workflow java.lang.String true message 0 'text/plain' 0 answer 0 UserNameHere 2011-03-16 12:02:48.666 CET net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeADR_substantiation_through_proteinsatc0eventType0event0eventName0cytoscape0drugTargetsOutput00diseaseProteinsOutput00CytoscapeResultGraph00diseaseProteins00drugTargets00connectingProteins00net.sf.taverna.t2.activitiesdataflow-activity1.2net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeCreateDrugTargetListstring0concatenated00fail00net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.StringListMerge workflow java.lang.String true string 0 l('text/plain') 0 concatenated 0 0 fail 0 UserNameHere 2011-01-27 12:48:44.599 CET UserNameHere 2011-01-27 12:54:47.847 CET UserNameHere 2011-03-16 11:56:59.109 CET UserNameHere 2011-03-16 12:35:02.385 CET UserNameHere 2011-02-10 11:14:16.435 CET UserNameHere 2011-02-10 11:26:20.837 CET UserNameHere 2011-01-27 12:48:28.442 CET UserNameHere 2011-01-27 12:58:24.852 CET UserNameHere 2011-01-27 14:01:57.290 CET UserNameHere 2011-03-16 12:43:23.121 CET net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetPathwaysproteinLists0intersectingPathways00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.WSDLActivity http://ibi.imim.es/axis2/services/AdrPathService?wsdl getPathways net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeCreateDiseaseProteinListstringADR_substantiation_through_proteinsdiseaseProteinsgenerateProteinListseventProteinsCreateDiseaseProteinListconcatenatedgenerateProteinListsdrugProteinsCreateDrugTargetListconcatenatedConvertToHTMLatcatcConvertToHTMLintersectingPathwaysgetPathwaysintersectingPathwaysConvertToHTMLeventeventNameCheckConnectingPathwaysintersectionListXPath_getPathwaysnodelistCheckConnectingPathwaysfailDiseaseCreateDiseaseProteinListfailCheckConnectingPathwaysfailDrugCreateDrugTargetListfailXPath_getPathwaysxpathxpath_valuevalueXPath_getPathwaysxml-textgetPathwaysintersectingPathwaysTellResultmessageCheckConnectingPathwaysresultADR_substantiation_through_proteinsatcatcADR_substantiation_through_proteinseventTypeeventTypeADR_substantiation_through_proteinseventeventADR_substantiation_through_proteinseventNameeventNameADR_substantiation_through_proteinscytoscapecytoscapeCreateDrugTargetListstringADR_substantiation_through_proteinsdrugTargetsgetPathwaysproteinListsgenerateProteinListsoutputdrugTargetsOutputADR_substantiation_through_proteinsdrugTargetsOutputdrugEventLinkingPathwaysConvertToHTMLEUADR_intersectingPathwayseventProteinsOutputADR_substantiation_through_proteinsdiseaseProteinsOutputdrugEventLinkingProteinsADR_substantiation_through_proteinsconnectingProteinsCytoscapeResultGraphADR_substantiation_through_proteinsCytoscapeResultGrapheventProteinsADR_substantiation_through_proteinsdiseaseProteinsdrugTargetsADR_substantiation_through_proteinsdrugTargets d471959c-29f3-49f6-bda2-5eaec8dd5ea8 2011-01-17 11:45:21.958 CET 32656a2e-ee50-4835-b479-aabc4396016f 2011-01-04 13:57:15.461 CET 653e4e25-055c-4379-9a83-2d1151d8478a 2011-01-14 18:14:09.85 CET 0ed622c5-32b6-4791-be7a-382da065f086 2010-12-20 16:03:47.872 CET 3f105056-fcab-4bc4-8cf8-9951729b24df 2011-01-04 12:17:29.826 CET 92b74c17-96d8-4934-8e8e-7a0a6e57cacc 2011-03-15 13:47:22.775 CET 8b7cf829-7859-420c-b9c8-01f98b083d36 2011-01-13 14:32:57.871 CET fddb1035-bbbc-4bf5-bef4-17698d5fc163 2011-01-24 17:17:23.149 CET cd0ec09d-4927-4e35-b871-c15f973ff63c 2011-07-29 16:01:09.361 CEST ADR_substantiaion 2011-03-03 17:19:02.318 CET f9ba5ab6-b688-47c5-b42a-043bc783a51e 2011-03-20 12:41:58.64 CET deb58f7d-9e66-44bb-b930-e5e49ea313cb 2010-12-20 15:29:06.561 CET ec1b8920-e38e-4fdf-810a-a2cadf481d9e 2011-04-15 13:32:07.580 CEST fee13559-e86b-4418-9599-f2a1d6446c75 2011-01-13 16:50:29.626 CET f2c45435-2f63-4179-879b-323954bcd773 2011-01-17 12:51:01.494 CET 9bbca5ad-5e2b-4342-981e-bdbbca78905f 2011-03-16 16:21:58.324 CET f9662ff3-5ad3-42ec-8930-68c628fd6502 2010-09-17 10:42:02.441 CEST e8d8164d-cf5a-43ae-8ca6-18becacf8d8b 2011-01-07 12:41:50.692 CET a58cc5d7-34ff-4249-847b-e7ac528a8b49 2011-02-11 17:55:26.353 CET cb84c608-6105-4b6b-9bb7-77acb56389ed 2010-09-17 10:52:24.545 CEST 7ab44917-a605-40c4-912d-ad115f75a315 2011-03-15 13:33:48.229 CET cba4e9b3-6dcb-4e2f-9ebe-08f42ed5bc38 2011-01-17 12:49:37.448 CET 37a82b12-5862-4b63-8ad6-aee20e96ba26 2011-03-15 13:38:22.610 CET 65e8de2b-f546-489c-a7b3-34e10fceadd4 2011-02-08 18:08:31.364 CET 88f58e58-6f9f-41fa-ac5c-2a24e20ed1ab 2011-02-08 17:23:11.786 CET 9d1b78c8-5d43-43cd-9e41-2c0d26290119 2011-01-17 10:57:16.237 CET 93d045f8-5566-400e-b931-2aca1f9b3947 2011-01-13 16:28:44.447 CET ce078332-d129-49d8-ac85-90387bfa67e3 2011-03-11 17:44:02.127 CET 554c0775-68cf-419c-8202-2f1baa1a9dca 2011-01-04 12:04:35.852 CET cc772697-d010-4057-b756-36c08166d645 2011-01-17 10:35:59.185 CET d7824096-eb0c-4fb9-87f5-0341596b5211 2010-09-17 10:48:39.9 CEST b66fe7cc-39dc-4949-afc0-83c195751d59 2011-01-04 17:36:27.395 CET 7a5af348-2104-49b8-b448-abf464cfa93a 2011-03-20 11:54:42.966 CET This workflow substantiates drug safety signals composed of a drug and an adverse reaction. In more detail, the workflow tries to find feasible paths connecting the drug and the event. First, it checks if there are proteins that are annotated to a given adverse event and at the same time target of the given drug. (NESTED WORKFLOW ADR_substantiation_through_proteins) Second, it tries to connect drug and event through biological pathways. Here, it checks if there are proteins from drug and event side which are expressed in the same tissue and also annotated to the same biological pathway. As adverse event, the following event types are allowed: 1) events as defined in the EU-ADR project such as UGIB 2) UMLS CUI concept identifiers As drug input 7 digit drug ATC codes are allowed. As result a list of intersecting proteins as well as a list of pathways is provided. If any of the two lists is not empty, the drug-event pair is substantiated as drug safety signal. For the intersecting proteins, a Cytoscape graph is generated for user-friendly visualization. It contains the event, drug and their annotated proteins as well as additional information such as links to publications etc. For the intersecting pathways a html page summarizing the results is generated. 2011-03-11 17:13:02.710 CET 3149dbd1-5026-465e-a23d-1e84cd2dd438 2011-03-16 12:03:06.361 CET Anna Bauer-Mehren Integrative Biomedical Informatics Laboratory (GRIB, IMIM/UPF) 2011-02-08 18:01:15.677 CET ff1f9074-7f1b-4f04-b09b-25e8d1075933 2011-01-17 11:08:52.797 CET ADR_substantiation 2011-03-10 11:38:43.750 CET e3312a5d-b3fc-4959-8201-679ca1cfe8c9 2011-03-16 12:13:58.439 CET e57ad22d-32f9-4fc7-80d1-9186a849119b 2011-01-07 15:27:40.662 CET f5f7d39a-e76c-4988-88a4-7d9e61f3b116 2011-01-04 12:59:27.437 CET 06b488ab-b4b6-4fdf-bf4e-557d1d5b0d2c 2011-01-04 16:21:31.258 CET e763f27d-93a2-4058-a2eb-4020c8773e5d 2011-02-08 17:30:54.650 CET 04df6bef-43a4-47c9-ab71-d835f232f82a 2011-03-16 12:35:06.863 CET Anna 2010-07-19 13:20:04.607 CEST 294b7d82-741e-4050-aabf-d92c099dcb76 2011-03-16 12:47:56.775 CET 2f799556-78fe-4d91-a0b9-989191ba3703 2011-01-13 16:39:50.188 CET a59568bd-3909-4380-a924-be18570272b5 2011-01-04 13:46:26.232 CET The signal substantiation workflow seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common among the proteins that are drug targets or metabolite targets and proteins associated to the clinical event (ii) through proteins that are drug targets or metabolite targets and proteins associated to the clinical event that participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are proteins that are annotated both to the clinical event and to the drug (NESTED WORKFLOW ADR_substantiation_through_proteins). Second, it looks for connections between the drug and the clinical event through biological pathways. Information about tissue expression of the proteins is used to filter the results. Input of the workflow: The input of the workflow is a drug-event pair. For the clinical events, the following types are allowed: 1) UMLS concept identifiers (UMLS CUI) 2) clinical events observed as adverse drug reactions according to the EU-ADR project (see http://ibi.imim.es/ADR_Substantiation.html for details) For the drug, a ATC code (5th level, seven digits) is required. NOTE: only one ATC code can be processed at a time Output of the workflow: 1) List of Drug-Event-Liniking proteins: The results can be visualized as a network using Cytoscape. The network is a multi-partite graph, in which the nodes are the event, the drug and the proteins, and the edges the associations between these nodes. In addition, all the evidences supporting the associations can be explored in the graph representation. 2)List of pathways: The results of the analysis through biological pathways is summarized in an html file. 2011-07-29 15:34:40.219 CEST 667271d2-597d-4625-91ce-d075886b89de 2011-01-04 13:51:48.724 CET 7d489ce0-6ed6-43d3-97fa-45fd176e818a 2010-09-30 17:57:08.458 CEST 66675211-5a30-4208-84ff-ff88264c56fd 2011-07-29 16:04:45.403 CEST 3037af44-07cf-46e1-ac3c-b91eafa75d74 2011-02-08 15:37:33.999 CET 7aa10c7d-6fe1-4b77-8808-7cffa61ae3db 2010-09-14 15:35:08.242 CEST 497d97fc-2cb4-499c-a839-51809a6b4654 2011-01-19 17:30:01.794 CET 0ea7d095-fc78-475b-9a96-efc6e41811dc 2011-01-04 15:43:14.845 CET 5c5101bf-6e14-400c-bcd6-66a7b4f6094b 2011-01-19 17:33:29.326 CET 8038ad73-2341-401f-9a99-1c9f30862a90 2011-01-07 11:04:15.227 CET e9ff23a5-0a75-45a8-80da-04db20f6e501 2011-04-15 09:57:29.858 CEST 2362930f-4165-4040-ae48-972079c15b99 2011-01-04 14:00:35.449 CET 6da62234-8122-49b8-84db-05d8fc69a0e2 2011-03-11 17:13:18.332 CET a4d41213-eac5-4218-9657-d335797ee624 2011-02-10 10:57:23.543 CET 3eefa652-556b-4bdb-8571-8916193fa47d 2011-02-11 17:20:11.19 CET 250f91b2-afa1-4bae-845a-a24cfb89a9bb 2011-02-11 17:43:44.119 CET 656f5a21-7dc4-4e46-a6e4-67fd197decfe 2011-01-14 18:08:30.745 CET 7b7bf9ce-5249-4ad0-af27-ef7987d5c051 2011-01-07 11:01:45.884 CET cbdfc13f-df16-4965-bc74-605d26c7d03f 2011-01-13 12:51:13.433 CET 90f41a2a-76c8-4de1-bdac-70a267ce9c3b 2011-03-15 13:33:13.917 CET 984a9292-80d5-4a03-bf77-cec858d566b3 2011-01-04 17:45:55.665 CET 2986cd93-b5b6-4d68-95ba-6d2e4863fbdd 2011-07-29 15:57:37.509 CEST 88fc305d-6670-4094-af52-29a51219a905 2011-02-04 15:35:17.39 CET baf8876d-4848-4588-a2bd-f5945bcd7467 2011-07-29 13:23:01.362 CEST 0ae6554a-e8e6-45ce-b37d-b9cbfe1f7a7e 2011-01-27 14:19:55.221 CET 0db3f322-5f1f-4505-bf6a-85c5a9eeb289 2011-01-04 12:48:54.533 CET ADR substantiation 2011-07-29 15:36:17.466 CEST 15d43d13-40f2-4306-b952-02c102c5c867 2011-01-27 14:41:42.46 CET The signal substantiation workflow seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common between the drug-target (ii) through proteins that are drug targets or metabolite targets and proteins associated to the clinical event that participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are proteins that are annotated both to the clinical event and to the drug (NESTED WORKFLOW ADR_substantiation_through_proteins). Second, it looks for connections between the drug and the clinical event through biological pathways. Information about tissue expression of the proteins is used to filter the results. Input of the workflow: The input of the workflow is a drug-event pair. For the clinical events, the following types are allowed: 1) UMLS concept identifiers (UMLS CUI), a single identifier of a list of identifiers are accepted. 2) clinical events observed as adverse drug reactions according to the EU-ADR project (see http://ibi.imim.es/ADR_Substantiation.html for details) For the drug, a ATC code (5th level, seven digits) is required. NOTE: only one ATC code can be processed at a time. Output of the workflow: 1) List of Drug-Event-Liniking proteins: The results can be visualized as a network using Cytoscape. The network is a multi-partite graph, in which the nodes are the event, the drug and the proteins, and the edges the associations between these nodes. In addition, all the evidences supporting the associations can be explored in the graph representation. 2)List of pathways: The results of the analysis through biological pathways is summarized in an html file. 2011-07-29 15:38:46.311 CEST 62ec5abb-7c12-4bb9-af57-456cbcbbda9e 2011-01-10 12:42:16.19 CET 31173be0-dbe9-4ece-b477-3693fa39a7ba 2011-07-29 17:38:51.793 CEST 04372b6f-fcc3-4b2c-83ac-b64512f59ce2 2010-09-17 10:39:50.849 CEST 776ad2f6-e9ba-4c99-ad3a-772b5e9cb61b 2010-12-21 15:39:22.876 CET 65eb78b5-485d-4cd9-9a11-7bddd846bbb6 2011-03-15 13:48:23.665 CET f941ca21-1633-4f04-81ef-b9ba74c78a34 2011-01-10 14:36:36.252 CET c4308939-a661-4907-8606-1a86778d8947 2010-07-29 18:24:46.817 CEST 15493c2e-a54c-493e-8898-710705b8c5d7 2010-09-08 16:38:16.856 CEST d19909e8-669b-4d65-9468-f760fd7fa750 2011-01-07 17:04:00.846 CET f6450ab7-d5fe-4ae5-b7f0-36f7a29cb8b4 2011-01-04 12:52:56.78 CET cad732c9-8359-465b-ba8c-b93fd44bfa54 2011-01-13 16:49:14.442 CET 5069111b-8740-4d87-8d97-67f945781f09 2011-01-27 14:12:18.422 CET 882c06d0-a11e-4967-a338-a8c67dfa4fb4 2010-08-26 19:22:46.869 CEST 935964c1-91b9-4e5f-9c32-ed5fccf9f9a2 2010-09-17 10:14:21.353 CEST 6e32b8bb-01e4-4abc-a589-2577b16b8f9c 2011-01-13 16:30:25.16 CET 46641391-2e52-4d10-826a-e096b79bec40 2011-02-08 17:40:06.602 CET cf360835-3b60-421b-a4a3-ff67fffa4aaf 2011-01-17 11:24:32.777 CET 11a2dca5-f9cc-4121-ac2d-1da011bf6ad8 2011-01-04 16:15:49.408 CET 218c5dcc-3492-4ba4-a473-9264f389058b 2011-01-17 12:43:10.315 CET 1897606e-1d7d-4c96-ab38-6ef1b9cf38ac 2010-09-30 18:05:13.306 CEST 55fe80fb-04d7-41e7-887b-51c79c87ac7e 2011-02-11 17:28:44.612 CET cd50768e-3d13-410b-81bf-69a54a7ca1be 2011-02-08 15:12:13.473 CET 09b3d4f2-ac6b-49de-bc63-c4fc83379834 2010-09-08 15:39:11.360 CEST 4f339317-dc4d-4151-8203-893f0e707b07 2011-01-07 15:23:18.432 CET df0821cc-9125-4b9a-aa73-2211758720bb 2011-02-08 17:49:18.886 CET 5b108f21-e22f-4d6c-b3a2-280552f43296 2011-01-13 16:16:16.29 CET af689045-45d3-4ca2-9e63-d833cdfd4803 2011-01-20 15:23:08.969 CET ae92fb5d-fd57-4faa-ba70-55607ed78347 2011-01-17 12:38:05.300 CET af060e60-6938-4295-8797-8c749b8d4085 2011-01-14 18:04:03.419 CET b80fba38-d085-4bef-924a-417825107648 2011-01-04 15:49:32.364 CET 2f700972-4f65-4993-9d83-d66122a57548 2011-01-13 16:13:22.795 CET a063837a-bf23-42da-8892-eb8044555c19 2010-09-30 18:08:32.887 CEST 698f8dc5-519d-42cd-9017-b0e7d12ef34a 2011-03-11 17:45:32.765 CET 0c323d59-b2a3-48b4-b7e4-be31aff18c8a 2011-02-08 17:55:36.60 CET 53503b95-945b-46d3-8663-5b176536f52c 2011-01-04 15:52:11.52 CET 36bfcc9d-c7ca-4be8-9253-4ffbce3c3e35 2011-02-11 17:15:22.568 CET ec258c77-f3a3-4657-9329-c820ab6870c6 2011-01-04 12:47:28.68 CET 85a3ae41-67b5-45fa-820d-912538444b1a 2011-01-13 12:45:21.974 CET 383b1299-9c53-4115-9343-608a3398d6ed 2011-03-16 16:27:15.122 CET 9e00fd8b-8dec-498c-a0dc-59d56ba02dc2 2011-02-08 18:34:28.770 CET fa61c748-de3c-4438-ad8a-33dd39fcb76f 2011-01-04 13:59:46.545 CET 37c313f4-fc7f-44fb-b486-75344db8f933 2011-01-13 15:50:00.475 CET 46c1500c-4932-4c68-aa8d-86bb7861dc90 2011-03-16 11:55:44.735 CET 72609134-3363-4249-8add-e09874606101 2011-01-07 13:00:06.54 CET b5507185-dd64-40aa-8e17-80cc8e6e5e86 2010-09-14 15:31:11.179 CEST 9f6fca78-6d4d-4e62-90d4-2211905b83f1 2011-01-21 14:20:14.134 CET 5f5a4dee-045f-4720-b990-9445ce4ce627 2010-09-30 18:03:28.544 CEST The signal substantiation workflow seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common among the proteins that are drug targets or metabolite targets and proteins associated to the clinical event (ii) through proteins that are drug targets or metabolite targets and proteins associated to the clinical event that participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are proteins that are annotated both to the clinical event and to the drug (NESTED WORKFLOW ADR_substantiation_through_proteins). Second, it looks for connections between the drug and the clinical event through biological pathways. Information about tissue expression of the proteins is used to filter the results. Input of the workflow: The input of the workflow is a drug-event pair. For the clinical events, the following types are allowed: 1) UMLS concept identifiers (UMLS CUI), a single identifier of a list of identifiers are accepted. 2) clinical events observed as adverse drug reactions according to the EU-ADR project (see http://ibi.imim.es/ADR_Substantiation.html for details) For the drug, a ATC code (5th level, seven digits) is required. NOTE: only one ATC code can be processed at a time. Output of the workflow: 1) List of Drug-Event-Liniking proteins: The results can be visualized as a network using Cytoscape. The network is a multi-partite graph, in which the nodes are the event, the drug and the proteins, and the edges the associations between these nodes. In addition, all the evidences supporting the associations can be explored in the graph representation. 2)List of pathways: The results of the analysis through biological pathways is summarized in an html file. 2011-07-29 15:35:53.809 CEST 0b1a7caa-589a-4fe2-a52c-3b0611d4abb5 2011-01-24 17:14:53.841 CET 33baa09c-f0a1-42c7-add1-563f6b2541d2 2011-02-08 17:44:01.638 CET 2b00853f-d2b9-4986-8085-fc3de81a7693 2010-09-08 17:25:02.20 CEST 304ef1c5-fee1-4c6d-9d22-2b0a8b3285fc 2011-01-17 12:50:25.677 CET de97e1d3-167f-4dae-917d-197e2e4b27b3 2010-09-30 18:00:40.4 CEST 86ef6f43-c15f-4c2b-940a-1a73704cbaac 2011-01-10 12:49:33.152 CET The signal substantiation workflow seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common among the proteins that are drug targets or metabolite targets and proteins associated to the clinical event (ii) through proteins that are drug targets or metabolite targets and proteins associated to the clinical event that participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are proteins that are annotated both to the clinical event and to the drug (NESTED WORKFLOW ADR_substantiation_through_proteins) Second, it looks for connections between the drug and the clinical event through biological pathways. Information about tissue expression of the proteins is used to filter the results Input of the workflow The input of the workflow is a drug-event pair. For the clinical events, the following types are allowed: 1) UMLS CUI concept identifiers (single identifier or a list of identifiers 2) clinical events observed as adverse drug reactions according to the EU-ADR project For the drug, a ATC code (7 digit level) is required Output of the workflow As result a list of connecting proteins as well as a list of pathways is provided. The results can be visualized as a network using Cytoscape. The network is a multi-partite graph, in which the nodes are the event, the drug and the proteins, and the edges the associations between these nodes. In addition, all the evidences supporting the associations can be explored in the graph representation. The results of the analyisis through biological pathways is summarized in an html file. 2011-03-11 17:27:32.929 CET 4b08aa99-b8dc-4318-9bf3-0cf0350ab3b2 2011-01-04 17:43:08.489 CET 14abaab8-def4-4893-bd09-0243317c3a2f 2011-02-10 10:36:57.584 CET 2720a061-814b-4cf5-9d49-653a1c738e37 2010-07-29 09:51:48.234 CEST 1b8280dd-fcd2-4f10-bdd9-3159f0cf3a9e 2011-02-10 10:31:55.239 CET dcc4c0b1-0b8a-4c90-92af-ea02dc89e48f 2011-04-18 17:30:43.73 CEST 0c4617d8-938b-497a-bd9b-e24a88881333 2010-09-17 10:49:31.705 CEST 2f0b90b4-41c1-4675-bbbb-37ee904f88b4 2011-01-14 18:10:30.484 CET 4780f614-18eb-4264-ab87-5b53914f7f08 2011-07-29 15:43:04.301 CEST 841e6b3c-7b1b-4e30-a333-d4876429e1f2 2011-01-13 15:08:13.15 CET ed4d02f5-5289-42ac-aa18-6939e670363b 2011-01-07 11:05:51.928 CET The signal substantiation workflow seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common among the proteins that are drug targets or metabolite targets and proteins associated to the clinical event (ii) through proteins that are drug targets or metabolite targets and proteins associated to the clinical event that participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are proteins that are annotated both to the clinical event and to the drug (NESTED WORKFLOW ADR_substantiation_through_proteins). Second, it looks for connections between the drug and the clinical event through biological pathways. Information about tissue expression of the proteins is used to filter the results. Input of the workflow: The input of the workflow is a drug-event pair. For the clinical events, the following types are allowed: 1) UMLS concept identifiers (UMLS CUI) 2) clinical events observed as adverse drug reactions according to the EU-ADR project (see for details) For the drug, a ATC code (5th level, seven digits) is required. NOTE: only one ATC code can be processed at a time Output of the workflow As result a list of connecting proteins as well as a list of pathways is provided. The results can be visualized as a network using Cytoscape. The network is a multi-partite graph, in which the nodes are the event, the drug and the proteins, and the edges the associations between these nodes. In addition, all the evidences supporting the associations can be explored in the graph representation. The results of the analysis through biological pathways is summarized in an html file. 2011-07-29 15:31:15.587 CEST EU-ADR IMIM 2010-07-19 13:20:24.541 CEST 260f0cc1-0e85-44d3-83fc-9efa5c72fdea 2011-03-11 18:06:26.209 CET bf84dfe6-5cbe-488b-86e4-4a71ece58e69 2010-09-08 15:35:53.307 CEST 2fe89980-66f4-4bea-9c9e-c28ef4ea10ac 2011-01-24 17:10:29.201 CET 21f344c5-c9f9-4801-af16-599fec21492b 2011-01-13 16:32:59.459 CET Anna Bauer-Mehren 2010-07-19 13:20:18.173 CEST e6af487b-f382-43ce-89fd-1760fb3e11bd 2011-03-11 18:10:19.899 CET 4346eb60-27f6-4c39-8492-3b400affc3fa 2011-02-08 17:23:41.806 CET Anna Bauer-Mehren Integrative Biomedical Informatics Laboratory (GRIB, IMIM-Hospital del Mar, UPF), Barcelona, Spain. This workflow is distributed under the GNU GPL licence (http://www.gnu.org/licenses/gpl.html). 2011-07-29 15:55:07.542 CEST 3d05b413-9350-46d1-afae-f1db198659c7 2010-09-17 10:40:56.793 CEST d5bc6c59-70e8-43fe-9212-191b0040b888 2011-01-04 11:45:28.859 CET b395013e-3879-47e8-822a-18a8a2d43149 2011-01-04 17:41:43.118 CET 510cab98-882c-4510-8959-fdbc3432fe9a 2011-02-04 15:29:18.911 CET 64f4a75e-d537-42bb-85fd-895bd35969c2 2011-01-13 15:54:42.790 CET eef744ef-73f2-46c4-a707-9dde6e6989ae 2011-01-24 15:28:34.452 CET f4184e56-45ab-4ca0-96f7-4f697a7c2f70 2011-01-27 14:50:24.104 CET The signal substantiation workflow seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common among the proteins that are drug targets or metabolite targets and proteins associated to the clinical event (ii) through proteins that are drug targets or metabolite targets and proteins associated to the clinical event that participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are proteins that are annotated both to the clinical event and to the drug (NESTED WORKFLOW ADR_substantiation_through_proteins) Second, it tries to connect drug and event through biological pathways. Here, it checks if there are proteins from drug and event side which are expressed in the same tissue and also annotated to the same biological pathway. As adverse event, the following event types are allowed: 1) events as defined in the EU-ADR project such as UGIB 2) UMLS CUI concept identifiers As drug input 7 digit drug ATC codes are allowed. As result a list of intersecting proteins as well as a list of pathways is provided. If any of the two lists is not empty, the drug-event pair is substantiated as drug safety signal. For the intersecting proteins, a Cytoscape graph is generated for user-friendly visualization. It contains the event, drug and their annotated proteins as well as additional information such as links to publications etc. For the intersecting pathways a html page summarizing the results is generated. 2011-03-11 17:16:15.257 CET a41f5504-baa0-4b99-81ab-f0fef1234979 2011-03-16 12:43:42.391 CET Anna Bauer-Mehren Integrative Biomedical Informatics Laboratory (GRIB, IMIM/UPF), Barcelona, Spain 2011-03-01 10:50:38.460 CET 4f30225c-d702-48ee-9c94-0b631e30f7ed 2011-02-07 16:16:31.810 CET The signal substantiation workflow seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common among the proteins that are drug targets or metabolite targets and proteins associated to the clinical event (ii) through proteins that are drug targets or metabolite targets and proteins associated to the clinical event that participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are proteins that are annotated both to the clinical event and to the drug (NESTED WORKFLOW ADR_substantiation_through_proteins) Second, it looks for connections between the drug and the clinical event through biological pathways. Information about tissue expression of the proteins is used to filter the results Input of the workflow The input of the workflow is a drug-event pair. For the clinical events, the following types are allowed: 1) UMLS CUI concept identifiers (single identifier or a list of identifiers) 2) clinical events observed as adverse drug reactions according to the EU-ADR project (see "Bauer-Mehren A, van Mullingen E, Carrascosa MC, Lopes P, Oliveira JL, Avillach P, Gayo Diallo, Mestres J, Boyer S, Sanz F, Kors J, Furlong LI. Workflows for the automatic filtering and substantiation of drug safety signals, 2011" for details) For the drug, a ATC code (5th level, seven digits) is required. Output of the workflow As result a list of connecting proteins as well as a list of pathways is provided. The results can be visualized as a network using Cytoscape. The network is a multi-partite graph, in which the nodes are the event, the drug and the proteins, and the edges the associations between these nodes. In addition, all the evidences supporting the associations can be explored in the graph representation. The results of the analyisis through biological pathways is summarized in an html file. 2011-03-11 17:48:07.519 CET be6fdb73-7d48-4f77-9928-0fa22b8bd954 2011-07-29 15:48:53.988 CEST 9ff8bd28-c30e-4a3a-a0c0-244875db38d1 2011-07-29 15:34:41.634 CEST ae84b161-c6b7-4b21-9f75-2497845699a9 2011-02-10 11:14:48.730 CET 97d747e1-bd62-4a94-bef0-f31729f898fc 2011-03-01 10:51:28.485 CET 58bbae56-adfb-44c2-9b50-0a055c655970 2011-01-17 10:38:00.451 CET 29f2b085-a292-4a86-8d90-2e9a96566428 2011-02-10 11:26:28.282 CET d42fa9b2-722c-4842-b57a-d66e98a65156 2011-01-17 12:36:51.706 CET 96b888b5-0878-4702-84d0-447e7907feec 2011-01-04 16:34:24.129 CET f9b47244-65d6-4589-8718-b5e33ef485bd 2011-01-13 16:38:20.39 CET 0095e0ec-82cd-49ab-9e01-60bdd3817224 2011-01-24 15:32:15.832 CET Anna Bauer-Mehren Integrative Biomedical Informatics Laboratory (GRIB, IMIM-Hospital del Mar, UPF), Barcelona, Spain. This workflow distributed under the GNU GPL licence (http://www.gnu.org/licenses/gpl.html). 2011-07-29 15:48:53.589 CEST e2c37fc0-0f67-4d25-8cbb-b37672fc6f19 2011-01-21 14:21:30.282 CET 7a29253f-18a9-4d66-bc12-b0ba27158309 2011-01-10 12:49:12.709 CET 4513d220-c9b3-4c07-8448-554009484ead 2011-02-10 11:37:58.38 CET 77ddd0cf-245b-4f5e-b041-57f40add0723 2011-02-10 11:34:34.773 CET 42b2ed0c-0986-4653-b953-a0514a4849d0 2011-01-24 15:29:05.764 CET 69676201-0660-4b18-9e0f-5f103d467523 2011-01-13 16:31:34.241 CET 8e17ab19-7c07-4906-a32f-a416f706188d 2010-09-08 15:34:46.474 CEST 2af370dd-e15f-452d-849d-201f71969672 2011-02-08 17:31:49.61 CET c4abbd34-6df9-47ea-acdc-18161d73f58c 2011-03-10 11:38:51.140 CET a76a5bbb-91e9-4b5b-b371-83adbb3c2f00 2011-01-13 15:56:40.508 CET 4a634e4a-1597-4a81-8791-c5fd2f6259bb 2011-07-29 15:41:07.553 CEST 7ff8652c-45ab-446f-b865-79c80d90880a 2011-01-17 14:06:06.709 CET 0ee7519a-82a4-4f8f-ac1e-6b4a0af1ca8c 2011-04-15 09:56:30.896 CEST bbb9fd64-fe0e-4bb4-9604-ec046550ce02 2011-07-29 15:35:57.399 CEST 220f1971-ff47-41eb-84a2-129aca61874b 2011-01-27 14:13:58.356 CET EUADR IBI-CGL signal substantiation through pathways 2011-02-08 18:02:07.470 CET 86bbb993-bfd1-455c-ad86-34cd0bf012af 2011-02-08 17:29:56.605 CET 37da3e95-eeed-450f-bf0a-9037a652e500 2011-01-24 17:29:39.214 CET 8cefd2ea-bd66-440a-851d-f6cf69e2ec82 2011-03-11 18:08:46.493 CET 055460a6-d3fe-4572-8acc-b0cb52a80e5b 2011-01-27 14:31:51.598 CET d46cd2df-d9a7-4508-9364-bc45cbe8158e 2011-01-13 16:20:17.110 CET a75d9a51-eff5-406c-87e4-9b819a305c0b 2011-01-04 11:19:54.815 CET 314d80ed-264b-4396-a047-2f628bea9161 2010-09-17 10:43:21.150 CEST 1f1150d1-7d13-40de-bb63-b522fe0cc527 2011-03-16 12:31:21.793 CET 2a0e987e-189e-485c-9a44-b13fb379d459 2010-12-21 15:44:16.508 CET 8c38e822-a0f2-410e-85ee-91323183e0e0 2011-01-24 17:15:33.722 CET f59f4c3a-a7d6-4df8-bf54-20cd54c95bad 2011-01-04 13:53:35.962 CET b56066b4-fe8d-456a-a6b5-8487fb0f239c 2011-02-08 18:02:49.55 CET 26f73c21-400f-4c63-8b61-ca6d410a49ca 2011-01-04 15:44:49.895 CET c95961bd-86db-47c8-9496-19da4b9c556e 2011-03-11 18:04:51.917 CET bac7b5d0-0dce-4c32-9939-6c46467be64d 2011-02-11 17:57:28.182 CET bce8d803-d64b-434f-af97-31aebc72300a 2011-01-14 18:06:06.550 CET 7dcbaabc-a79e-4438-8203-cfd54c97445f 2011-01-21 14:43:56.580 CET The signal substantiation workflow seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common among the proteins that are drug targets or metabolite targets and proteins associated to the clinical event (ii) through proteins that are drug targets or metabolite targets and proteins associated to the clinical event that participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are proteins that are annotated both to the clinical event and to the drug (NESTED WORKFLOW ADR_substantiation_through_proteins) Second, it looks for connections between the drug and the clinical event through biological pathways. Information about tissue expression of the proteins is used to filter the results Input of the workflow The input of the workflow is a drug-event pair. For the clinical events, the following types are allowed: 1) UMLS CUI concept identifiers (single identifier or a list of identifiers 2) clinical events observed as adverse drug reactions according to the EU-ADR project For the drug, a ATC code (5th level, seven digits) is required. Output of the workflow As result a list of connecting proteins as well as a list of pathways is provided. The results can be visualized as a network using Cytoscape. The network is a multi-partite graph, in which the nodes are the event, the drug and the proteins, and the edges the associations between these nodes. In addition, all the evidences supporting the associations can be explored in the graph representation. The results of the analyisis through biological pathways is summarized in an html file. 2011-03-11 17:29:48.732 CET fc036ee8-4923-46c9-ab97-48fd1d0edba4 2011-01-04 17:35:51.643 CET d9173713-01e6-42cc-a1e3-cbf3ef27a6b3 2011-01-13 14:48:14.496 CET 5b69bd99-3672-45f0-9518-c0186ea88345 2011-01-25 09:30:05.429 CET f487558d-5599-490a-9c57-8eeb3f9537ac 2010-09-30 18:11:10.559 CEST 4183fd75-868c-4209-9b1f-1a6983402288 2010-09-17 10:44:54.881 CEST 658773b8-c856-4e48-a0b8-50e41be3d69d 2010-12-20 15:49:39.984 CET 9aa3115d-bd94-4143-9527-a47bdbda1c3e 2010-09-08 17:07:48.587 CEST 88f4c8d8-44e3-46c7-8a2c-54f67b937982 2011-01-27 14:45:00.403 CET ee4f5456-69c2-41e9-af9d-94e919a4f01a 2011-01-14 18:13:16.336 CET Signal substantiation through proteins and pathways 2011-03-01 10:50:53.142 CET f13ae848-8516-4192-9e86-4aff2853694d 2011-01-07 13:02:55.763 CET c37dbf69-e5ac-451a-b579-163c7ac5d665 2011-01-17 10:32:32.30 CET 88f6405e-9afb-4f26-9a78-36c60e5a4dcd 2011-01-17 12:32:11.716 CET da9c07a9-50c8-4d2f-9fe2-01ac2b82666e 2011-03-16 11:45:43.687 CET fca2019e-0450-45b8-8f43-9d05583f5698 2011-02-08 17:38:35.876 CET 423144e5-b1a3-44e0-a4c7-2033e1118085 2011-01-07 13:14:01.754 CET 5625eddc-85bc-4748-a9d4-fea753e8860f 2011-01-04 12:06:44.735 CET 21e4c0a6-9a6c-4460-9c47-127288c8b219 2011-01-07 17:01:53.65 CET 23016ee1-4112-467f-8d95-7a0fccec501d 2011-01-13 15:52:05.450 CET 1b852c51-9908-46b1-b68c-3f169682f23e 2011-01-17 12:09:55.130 CET a4c22227-00af-4525-bd90-2741da71a846 2010-09-30 17:59:44.739 CEST The signal substantiation workflow seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common among the proteins that are drug targets or metabolite targets and proteins associated to the clinical event (ii) through proteins that are drug targets or metabolite targets and proteins associated to the clinical event that participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are proteins that are annotated both to the clinical event and to the drug (NESTED WORKFLOW ADR_substantiation_through_proteins). Second, it looks for connections between the drug and the clinical event through biological pathways. Information about tissue expression of the proteins is used to filter the results. Input of the workflow: The input of the workflow is a drug-event pair. For the clinical events, the following types are allowed: 1) UMLS concept identifiers (UMLS CUI), a single identifier of a list of identifiers are accepted. 2) clinical events observed as adverse drug reactions according to the EU-ADR project (see http://ibi.imim.es/ADR_Substantiation.html for details) For the drug, a ATC code (5th level, seven digits) is required. NOTE: only one ATC code can be processed at a time. Output of the workflow: 1) List of Drug-Event-Liniking proteins: The results can be visualized as a network using Cytoscape. The network is a multi-partite graph, in which the nodes are the event, the drug and the proteins, and the edges the associations between these nodes. In addition, all the evidences supporting the associations can be explored in the graph representation. 2)List of pathways: The results of the analysis through biological pathways is summarized in an html file. 2011-07-29 15:38:07.333 CEST 8605e865-958b-4f8e-834e-2806d9b1582e 2011-01-07 11:06:46.487 CET ea3c8053-5bbe-4e33-bd69-2959d54efd11 2011-01-13 16:18:36.312 CET 22bbbb79-c782-4b30-8f56-94997ae64f87 2011-02-08 17:59:04.315 CET a12cecc7-2962-4b13-89d5-3b60eaf69648 2011-01-04 12:56:07.950 CET b7af5884-8ad6-4201-a2b5-6d7a2d6160ad 2010-09-08 15:45:03.444 CEST The signal substantiation workflow seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common among the proteins that are drug targets or metabolite targets and proteins associated to the clinical event (ii) through proteins that are drug targets or metabolite targets and proteins associated to the clinical event that participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are proteins that are annotated both to the clinical event and to the drug (NESTED WORKFLOW ADR_substantiation_through_proteins) Second, it lootries to connect drug and event through biological pathways. Here, it checks if there are proteins from drug and event side which are expressed in the same tissue and also annotated to the same biological pathway. As adverse event, the following event types are allowed: 1) events as defined in the EU-ADR project such as UGIB 2) UMLS CUI concept identifiers As drug input 7 digit drug ATC codes are allowed. As result a list of intersecting proteins as well as a list of pathways is provided. If any of the two lists is not empty, the drug-event pair is substantiated as drug safety signal. For the intersecting proteins, a Cytoscape graph is generated for user-friendly visualization. It contains the event, drug and their annotated proteins as well as additional information such as links to publications etc. For the intersecting pathways a html page summarizing the results is generated. 2011-03-11 17:17:27.733 CET 501fec94-9965-4157-b32e-867a106712f3 2011-01-14 18:22:44.494 CET 5c12e2cd-c510-4478-bda2-31d5092e0a0a 2011-03-03 17:31:49.398 CET d08bc93b-51c4-4c40-bd72-11d549c32ead 2011-01-13 14:06:02.321 CET e64aa3ae-eea5-4175-9d7f-21c3e04c9952 2011-01-27 14:16:52.272 CET 1a2f5201-4619-486d-9954-2be1741631b1 2011-03-11 18:03:10.628 CET ae013666-d74a-4624-ab6d-2d39db1ec8b0 2011-01-27 14:02:11.88 CET 151afddc-dd5c-4ed2-beb8-131785f2b8bb 2011-04-18 17:32:11.514 CEST 44ef6149-c0e2-4466-90b2-f13051fbe7ca 2011-01-13 15:49:08.268 CET 1bcb72f3-d887-46db-8987-5110137dee7c 2011-01-13 16:56:08.617 CET baedf8f8-43c9-41f8-b5f8-2be50598b57a 2011-07-29 16:38:30.656 CEST e5ff72f4-929a-47fb-8592-cae2dbbbd2e0 2011-01-14 18:29:12.87 CET 53931c4d-2c75-4148-acde-8f69bb7fd626 2011-01-14 18:03:03.413 CET c73e86bd-e273-493b-9d5c-b8745dff38a0 2011-07-29 15:58:41.698 CEST a902b378-4626-4df8-809a-93123c33c9a9 2011-01-04 12:15:24.2 CET cc468b4a-24fe-4463-ad13-fec4ff026441 2011-01-04 11:14:23.26 CET 24cb7be8-e08f-4491-8bf8-35b00b118495 2010-08-26 16:41:14.887 CEST 0ae5c9ec-423a-42eb-ba9a-be3c9e02f323 2011-01-27 12:55:00.403 CET 39610a7c-e061-4f9d-bd80-88309bbd6ab9 2011-01-17 11:32:10.27 CET 5e2ff5a7-5420-4e9f-b02e-114a8e2dc863 2011-02-08 14:40:24.758 CET 78c2ffad-6362-4ab3-b4b7-934b210ef48b 2010-12-20 15:33:23.98 CET e33179de-2871-42c8-8cb1-f04b8e649181 2011-01-27 12:47:09.176 CET 4d1f9484-623d-40a4-bd35-a7ae46759706 2011-02-08 18:01:45.640 CET 87ce4583-2a1f-477c-9c17-9253f6bf35b9 2010-09-14 15:33:56.170 CEST 9c0b50d0-9972-4be4-9fdd-81eeb5643dff 2011-01-27 14:25:54.843 CET f2f5f285-9c68-4a07-a77e-ffc3995a8738 2011-01-04 13:44:31.852 CET bfb6d7b3-3dd3-43f4-866d-10d2d658bd9a 2010-12-22 11:59:44.908 CET 55639062-218e-41bb-839e-d2c3d4659a1c 2010-08-26 17:15:56.889 CEST Anna Bauer-Mehren Integrative Biomedical Informatics Laboratory (GRIB, IMIM-Hospital del Mar, UPF), Barcelona, Spain 2011-03-11 17:17:25.944 CET b0ee9766-858e-46f7-a2cb-d38178b66a24 2011-01-13 14:29:33.126 CET 9c33a4c4-433f-491f-8dc5-573094ea6e71 2011-03-11 17:29:53.532 CET 6dfd8b4c-94c4-4c81-b9a2-426ef3cf6a4a 2011-02-08 17:22:24.892 CET 58589cdb-d8d6-45a3-83c5-116afa1f09d3 2011-01-17 14:03:03.793 CET 4a5833ed-2c3c-4fbb-9f4e-0cf112d4eb4e 2011-03-11 17:27:44.735 CET de788bee-1e95-4c28-a5b6-0730d2feea47 2011-07-29 17:34:54.170 CEST fc614a9b-6d64-47a1-8ec9-1e0906f169a2 2011-03-16 15:43:22.514 CET 1dfeeb2f-41ee-445d-b780-38367b4bcc78 2010-09-30 17:58:44.713 CEST b8238866-091e-4bfd-8b53-3169af5e67ae 2011-01-04 12:09:27.450 CET b54625a7-01c7-451c-9c07-2e97ae8ba326 2011-01-04 12:57:37.762 CET The signal substantiation workflow seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common between the drug-target and the event-protein profiles. (ii) assessing if the proteins in the drug-target profile and in the event-protein profile participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are proteins that are annotated both to the clinical event and to the drug (NESTED WORKFLOW ADR_substantiation_through_proteins). Second, it looks for connections between the drug and the clinical event through biological pathways. Information about tissue expression of the proteins is used to filter the results. Input of the workflow: The input of the workflow is a drug-event pair. For the clinical events, the following types are allowed: 1) UMLS concept identifiers (UMLS CUI), a single identifier of a list of identifiers are accepted. 2) clinical events observed as adverse drug reactions according to the EU-ADR project (see http://ibi.imim.es/ADR_Substantiation.html for details) For the drug, an ATC code (5th level, seven digits) is required. NOTE: only one ATC code can be processed at a time. Output of the workflow: 1) List of Drug-Event-Liniking proteins: The list of proteins that link the drug with the event. The results can be visualized as a network using Cytoscape. The network is a multi-partite graph, in which the nodes are the event, the drug and the proteins, and the edges the associations between these nodes. In addition, all the evidences supporting the associations can be explored in the graph representation. 2)List of pathways: The list of pathways from Reactome that connect the drug and the event. The results of the analysis through biological pathways is summarized in an html file. 2011-07-29 15:43:00.221 CEST 30a8edbd-e0e9-45b9-9bd5-d879e8ff21d8 2011-01-27 12:58:43.572 CET 39cc5e6e-78d7-4866-9e66-3ca38fbd08ec 2011-03-11 17:48:10.78 CET fce0bbbe-4c42-427c-96f2-5240cbb65fca 2011-02-11 17:30:43.102 CET The signal substantiation workflow seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common between the drug-target and the event-protein profiles. (ii) assessing if the proteins in the drug-target profile and in the event-protein profile participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are proteins that are annotated both to the clinical event and to the drug (NESTED WORKFLOW ADR_substantiation_through_proteins). Second, it looks for connections between the drug and the clinical event through biological pathways. Information about tissue expression of the proteins is used to filter the results. Input of the workflow: The input of the workflow is a drug-event pair. For the clinical events, the following types are allowed: 1) UMLS concept identifiers (UMLS CUI), a single identifier of a list of identifiers are accepted. 2) clinical events observed as adverse drug reactions according to the EU-ADR project (see http://ibi.imim.es/ADR_Substantiation.html for details) For the drug, a ATC code (5th level, seven digits) is required. NOTE: only one ATC code can be processed at a time. Output of the workflow: 1) List of Drug-Event-Liniking proteins: The results can be visualized as a network using Cytoscape. The network is a multi-partite graph, in which the nodes are the event, the drug and the proteins, and the edges the associations between these nodes. In addition, all the evidences supporting the associations can be explored in the graph representation. 2)List of pathways: The results of the analysis through biological pathways is summarized in an html file. 2011-07-29 15:41:05.349 CEST c5771cbe-778c-4d6b-9f51-542995f8a23f 2011-02-09 11:13:11.570 CET cc8f4d14-0ace-4cc8-8fff-f96b78239046 2010-09-17 10:14:44.745 CEST cc3023d1-fed7-4870-8dd9-467cea4c01fe 2010-09-08 15:29:14.947 CEST df79c8c4-6777-48c5-9d59-00ccab13e43d 2011-01-04 16:13:26.111 CET a599c245-6cfe-43dd-b7d2-19c14af0f74c 2011-03-15 13:36:17.408 CET 843affcb-828f-4624-852b-a2e99dda68ea 2011-01-04 16:06:49.11 CET f25c3841-8afe-4c63-94be-d2d454ddbf48 2011-01-24 12:30:57.285 CET 71fee83a-3325-45d9-bd0a-48587b3f48a8 2011-07-29 13:31:09.487 CEST 3b5e0702-3362-4022-9f9b-453acf20494e 2011-01-04 16:10:11.817 CET ec1e578a-6980-4a25-8a64-471a590d70c4 2011-01-07 13:22:32.167 CET a567a534-ba76-4fe9-9b1d-b535b46b8c30 2011-03-16 16:28:54.945 CET fcf5481e-d174-4011-a147-2b71d0a9c3b0 2011-03-11 17:50:43.833 CET a8565d7f-1947-49e1-9370-015e1f93b603 2011-01-07 12:32:28.763 CET 2fff42ee-f6f2-418e-8497-fd251d8aaf7d 2011-01-10 12:53:40.490 CET 92f5d4a5-e715-47fd-9566-d594c2c4b1fa 2011-07-29 15:55:52.426 CEST d927ef64-6cd0-45e8-ae2b-9ff77bc31765 2011-01-04 16:18:35.499 CET 6027b3fe-852f-425c-ae29-e863b1661433 2010-09-08 15:33:59.145 CEST 42096290-5966-4a5d-9919-1e278e1f9309 2011-03-11 17:59:15.996 CET 5ff684db-0eed-4796-8dc5-517f213b56a2 2011-01-10 10:27:14.753 CET bcf15876-78a9-4384-b1e6-3f5cc33ef605 2011-02-11 17:38:29.129 CET 69c9bf8b-a73f-4202-9294-21928d3c4a2c 2011-02-08 18:34:07.981 CET b87d929c-35cb-42b2-9b85-5da55b571720 2011-01-17 11:43:19.215 CET 37d45e5b-c0ef-4f73-9a69-9b1048f8cc67 2011-01-13 14:01:08.590 CET faa5e928-50d1-40db-a001-0b01d669c702 2011-03-16 12:47:19.911 CET ce77e21e-8c77-4206-a066-6c5b86e2d037 2011-03-11 17:28:58.743 CET 4d806381-6574-44f8-8a6d-b9112fb7cd4a 2011-03-11 17:16:21.275 CET d4af1b5a-8069-4f1b-8053-b93d773a4b79 2011-01-24 14:13:35.151 CET 5022eb2d-6711-4b4b-97e0-8c62f9776c45 2011-01-07 13:03:46.867 CET 639a0092-1856-4571-abac-489ec118f6ec 2011-02-08 18:16:17.218 CET This workflow checks if there are proteins that are annotated to a given adverse event and at the same time target of the given drug. (NESTED WORKFLOW EUADR_IBI_CGL_signal_substantiation_through_proteins) Moreover, it tries to connect drug and event through biological pathways. It checks if there are proteins, which are expressed in the same tissue and also annotated to the same pathway. As adverse event, the following event types are allowed: 1) events as defined in the EU-ADR project such as UGIB 2) UMLS CUI concept identifiers As drug input 7 digit drug ATC codes are allowed. As result a list of intersecting proteins as well as a list of intersecting pathways is provided. If any of the two lists is not empty, the drug-event pair is substantiated as signal. For the intersecting proteins, there is a Cytoscape graph is generated for user-friendly visualization. It contains the event, drug and their annotated proteins as well as additional information such as links to publications etc. For the intersecting pathways a html page summarizing the results is generated. 2011-02-08 18:14:22.946 CET a7637da4-1853-47eb-b6b6-6b6187de4968 2010-09-08 15:37:34.78 CEST f331ed5c-0969-4bb7-8888-69b3eccf80f9 2011-01-10 14:35:40.987 CET 0b2a507a-92f5-47ba-8507-22940d44dc71 2011-03-03 17:21:51.236 CET Anna Bauer-Mehren Integrative Biomedical Informatics Laboratory (GRIB, IMIM-Hospital del Mar, UPF), Barcelona, Spain. This workflow distributed under the GNU GPL licence. 2011-07-29 15:47:12.138 CEST 69d9e94d-4948-4cf2-93ae-a6bb2cd71a8a 2010-09-08 15:30:15.132 CEST 8eccba26-6a75-488f-a99e-e73d57d7b601 2011-01-05 17:56:23.509 CET 3a624094-ede6-414f-a630-772aec4839c1 2011-02-08 17:27:34.284 CET ab8a5018-e8a5-4518-8568-af60ea5aa611 2011-01-24 15:17:23.110 CET b6fd1029-7f31-49bc-9854-dda121d530f7 2011-03-11 17:54:35.277 CET d9244dcd-5e77-49c5-bd98-5778ffcbf7a1 2011-01-07 15:29:00.928 CET This workflow substantiates drug safety signals composed of a drug and an adverse reaction. In more detail, the workflow tries to find feasible paths connecting the drug and the event. First, it checks if there are proteins that are annotated to a given adverse event and at the same time target of the given drug. (NESTED WORKFLOW ADR_substantiation_through_proteins) Second, it tries to connect drug and event through biological pathways. Here, it checks if there are proteins from drug and event side which are expressed in the same tissue and also annotated to the same biological pathway. As adverse event, the following event types are allowed: 1) events as defined in the EU-ADR project such as UGIB 2) UMLS CUI concept identifiers As drug input 7 digit drug ATC codes are allowed. As result a list of intersecting proteins as well as a list of pathways is provided. If any of the two lists is not empty, the drug-event pair is substantiated as drug safety signal. For the intersecting proteins, a Cytoscape graph is generated for user-friendly visualization. It contains the event, drug and their annotated proteins as well as additional information such as links to publications etc. sFor the intersecting pathways a html page summarizing the results is generated. 2011-03-03 17:21:53.838 CET 0cf92a75-21ab-47be-9f1c-d413fbacd5da 2011-02-10 11:09:51.857 CET a44786bf-7821-4d57-b90b-5f54ea6fed27 2011-01-07 13:15:50.669 CET 2fc970ff-568d-4991-b44b-cf3081b98a50 2011-01-14 18:12:06.86 CET 2564f676-3ac1-404d-9f5c-c6da9750a0ee 2011-01-27 12:49:05.723 CET 9fe4accf-0799-41bc-b67c-83a641e8311f 2011-01-10 12:46:26.160 CET 52875587-1ece-41ba-b152-3142f162b754 2011-02-08 18:33:40.593 CET 2fda05ef-384b-45cb-9378-146f8d831b22 2011-02-09 11:13:47.210 CET 84cd4fd8-b1e6-4a0d-92e4-7b5fceda028f 2011-03-01 10:50:54.88 CET 0aabc0d8-a7bb-4b9b-a8aa-6d238ce4d7db 2010-08-26 19:24:05.143 CEST 646c546a-2c84-4ec5-84ad-53e28b453565 2011-07-29 13:22:46.915 CEST e98d765a-4eec-4f87-b05f-04c5591efc9a 2011-01-07 11:01:18.944 CET a59a2bab-0fc2-42fc-a036-3c11c376ec33 2011-01-24 14:13:23.143 CET af850d3a-cda3-469a-872f-97933edf8687 2011-03-11 17:53:11.310 CET c6d50660-c118-4896-8133-479b21f168b1 2010-09-30 18:06:34.340 CEST 5014d953-b1a6-4be6-82ca-989681510645 2011-01-14 18:31:49.315 CET e5acb382-1cf9-4792-ab8f-ba1ad87eef82 2011-01-04 14:04:01.351 CET 39d7d995-6fdd-4a26-8418-fa1d5ea8c649 2011-03-03 17:34:35.658 CET 7e527514-eeff-4319-b83b-72c529dfff7f 2011-03-16 16:24:32.259 CET b684b5a4-aba5-43ba-a98e-d3b7a6b08be9 2011-02-08 15:44:37.643 CET 8953bc2a-c768-4876-838b-b90aa79254ac 2010-09-08 16:31:59.996 CEST The signal substantiation workflow seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common between the drug-target and the event-protein profiles. (ii) through proteins that are drug targets or metabolite targets and proteins associated to the clinical event that participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are proteins that are annotated both to the clinical event and to the drug (NESTED WORKFLOW ADR_substantiation_through_proteins). Second, it looks for connections between the drug and the clinical event through biological pathways. Information about tissue expression of the proteins is used to filter the results. Input of the workflow: The input of the workflow is a drug-event pair. For the clinical events, the following types are allowed: 1) UMLS concept identifiers (UMLS CUI), a single identifier of a list of identifiers are accepted. 2) clinical events observed as adverse drug reactions according to the EU-ADR project (see http://ibi.imim.es/ADR_Substantiation.html for details) For the drug, a ATC code (5th level, seven digits) is required. NOTE: only one ATC code can be processed at a time. Output of the workflow: 1) List of Drug-Event-Liniking proteins: The results can be visualized as a network using Cytoscape. The network is a multi-partite graph, in which the nodes are the event, the drug and the proteins, and the edges the associations between these nodes. In addition, all the evidences supporting the associations can be explored in the graph representation. 2)List of pathways: The results of the analysis through biological pathways is summarized in an html file. 2011-07-29 15:39:10.491 CEST The signal substantiation workflow seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common among the proteins that are drug targets or metabolite targets and proteins associated to the clinical event (ii) through proteins that are drug targets or metabolite targets and proteins associated to the clinical event that participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are proteins that are annotated both to the clinical event and to the drug (NESTED WORKFLOW ADR_substantiation_through_proteins) Second, it looks for connections between the drug and the clinical event through biological pathways. Information about tissue expression of the proteins is used to filter the results Input of the workflow The input of the workflow is a drug-event pair. For the clinical events, the following types are allowed: 1) UMLS CUI concept identifiers (single identifier or a list of identifiers) 2) clinical events observed as adverse drug reactions according to the EU-ADR project (see ref. for details) For the drug, a ATC code (5th level, seven digits) is required. NOTE: only one ATC code can be processed at a time Output of the workflow As result a list of connecting proteins as well as a list of pathways is provided. The results can be visualized as a network using Cytoscape. The network is a multi-partite graph, in which the nodes are the event, the drug and the proteins, and the edges the associations between these nodes. In addition, all the evidences supporting the associations can be explored in the graph representation. The results of the analysis through biological pathways is summarized in an html file. 2011-03-15 13:45:23.148 CET The signal substantiation workflow seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common among the proteins that are drug targets or metabolite targets and proteins associated to the clinical event (ii) through proteins that are drug targets or metabolite targets and proteins associated to the clinical event that participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are proteins that are annotated both to the clinical event and to the drug (NESTED WORKFLOW ADR_substantiation_through_proteins) Second, it looks for connections between the drug and the clinical event through biological pathways. Information about tissue expression of the proteins is used to filter the results Input of the workflow The input of the workflow is a drug-event pair. For the clinical events, the following types are allowed: 1) UMLS CUI concept identifiers (single identifier or a list of identifiers 2) clinical events observed as adverse drug reactions according to the EU-ADR project For the drug, a ATC code (7 digit level) is required. Output of the workflow As result a list of connecting proteins as well as a list of pathways is provided. The results can be visualized as a network using Cytoscape. The network is a multi-partite graph, in which the nodes are the event, the drug and the proteins, and the edges the associations between these nodes. In addition, all the evidences supporting the associations can be explored in the graph representation. The results of the analyisis through biological pathways is summarized in an html file. 2011-03-11 17:28:52.916 CET dd6c4837-c654-4f83-912e-d46922e0e0a0 2010-09-08 17:08:39.265 CEST 3edb1d6f-00b2-45d6-94f9-c5b99d15f2eb 2010-09-17 10:53:44.129 CEST 54841a39-a37a-4b17-9e8b-5bd87f48c0b7 2011-02-08 14:46:45.233 CET dd12e38a-a639-4553-8fd5-fb278a79b444 2011-01-07 12:39:58.59 CET ADR_substantiation_through_proteinsatc00 Workflow ATC input 2010-07-19 13:19:29.11 CEST Workflow ATC input The 7 digit atc code of a drug 2011-02-08 18:23:38.437 CET M01AH01 2010-07-19 13:19:34.980 CEST event00 UGIB 2010-09-30 17:56:42.141 CEST Workflow event input 2010-09-30 17:56:35.723 CEST Workflow event input Allowed events are: 1) events of type EUADR_EVENT as defined in the EUADR project 2) events of type UMLS being a CUI concept identifier 2011-02-08 18:23:17.18 CET cytoscape00 /home/user/cytoscape-v2.7.0/ 2011-01-10 12:49:14.15 CET cytoscape-v2.7.0 2011-01-10 12:46:17.448 CET insert here the path to your local cytoscape installation e.g. /home/user/cytoscape 2011-01-10 12:45:49.862 CET insert here the path to your local cytoscape installation e.g. /home/user/cytoscape-v2.7.0/ 2011-01-10 12:49:09.100 CET Insert here the path to your local cytoscape installation e.g. /home/user/cytoscape-v2.7.0/ 2011-02-08 18:34:44.588 CET insert here the path to your local cytoscape installation e.g. /home/user/cytoscape-v2.7.0 2011-01-10 12:46:10.80 CET /home/user/cytoscape-v2.7.0 2011-01-10 12:46:23.859 CET eventType00 EUADR_EVENT 2011-02-08 15:47:54.714 CET Type of the event to be processed. Must be either EUADR_EVENT if the event is defined in the EUADR project or UMLS if the event is a list of CUI concept identifiers 2011-01-24 17:29:31.677 CET eventName00 UGIB 2011-02-08 16:00:45.505 CET Name of the event. This is only required for user-friendly visualization of the results. In particular, if the input is a CUI concept identifier. 2011-02-08 16:00:42.1 CET diseaseProteinsOutput Full XML output for the get Disease Associated genes web service. 2010-07-19 13:19:17.699 CEST Full XML output for the getDiseaseAssociatedProteins web service. 2011-02-08 18:26:03.240 CET drugTargetsOutput Full XML output for the get drug targets web service. 2010-07-19 13:17:52.912 CEST Full XML output for the getDrugTargets web service. 2011-02-08 18:26:57.248 CET connectingProteins List of proteins annotated to both, event and drug. 2011-02-08 18:27:43.676 CET CytoscapeResultGraph Cytoscape graph which can be openend in Cytoscape. Simply store this file using the file ending .xgmml and open it in Cytoscape. It contains the drug, event and their annotated proteins as well as supporting information such as link outs to publications etc. 2011-02-08 18:25:06.342 CET diseaseProteins List of all proteins annoated to the event. 2011-02-08 18:25:36.785 CET drugTargets List of proteins annotated to the drug. 2011-02-08 18:26:26.286 CET getSmileFromATCatc0smile00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.WSDLActivity http://cgl.imim.es/axis2/services/cglAlertService?wsdl getSmileFromATC net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetUniprotListFromSmilesmile0relationlist00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.WSDLActivity http://cgl.imim.es/axis2/services/cglAlertService?wsdl getUniprotListFromSmile net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeXPath_getDrugTargetsxml-text0xpath0nodelistAsXML11net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker dom4j:dom4j:1.6 workflow dom4j dom4j 1.6 716010169 java.lang.String true xpath 0 'text/plain' java.lang.String true xml-text 0 'text/xml' 1 nodelist 1 l('text/plain') 1 nodelistAsXML 1 l('text/plain') net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeXPath_getDiseaseProteinsxpath0xml-text0nodelistAsXML11net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker dom4j:dom4j:1.6 workflow dom4j dom4j 1.6 716010169 java.lang.String true xpath 0 'text/plain' java.lang.String true xml-text 0 'text/xml' 1 nodelist 1 l('text/plain') 1 nodelistAsXML 1 l('text/plain') net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeIntersectionlist21list11intersection11net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.StringSetIntersection workflow java.lang.String true list1 1 l('text/plain') java.lang.String true list2 1 l('text/plain') 1 intersection 1 UserNameHere 2011-03-15 16:02:54.411 CET UserNameHere 2011-03-15 15:55:03.945 CET UserNameHere 2011-03-15 16:17:09.846 CET UserNameHere 2011-03-15 15:54:57.504 CET net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeCheckConnectingProteinsintersectionList1fail0text0result00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true intersectionList 1 text/plain java.lang.String true text 0 text/plain java.lang.String true fail 0 text/plain 0 result 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRemove_Duplicate_DTstringlist1strippedlist11net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates workflow java.lang.String true stringlist 1 l('text/plain') 1 strippedlist 1 UserNameHere 2011-03-15 15:48:44.231 CET UserNameHere 2011-03-15 16:16:34.632 CET UserNameHere 2011-03-15 16:00:05.815 CET UserNameHere 2011-03-15 15:49:17.216 CET UserNameHere 2011-03-15 15:51:26.452 CET UserNameHere 2011-03-15 15:50:45.603 CET net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRemove_Duplicates_DPstringlist1strippedlist11net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates workflow java.lang.String true stringlist 1 l('text/plain') 1 strippedlist 1 UserNameHere 2011-03-15 15:51:13.700 CET UserNameHere 2011-03-15 15:51:04.806 CET UserNameHere 2011-03-15 15:47:36.710 CET UserNameHere 2011-03-15 16:00:18.151 CET UserNameHere 2011-03-15 16:15:50.837 CET net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeConvertToCytoscapeGraphdrugTargetOutput0cytoscape0atc0event0proteinDiseaseOutput0fail0EUADR_resultGraph00net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity net.sourceforge.taverna.scuflworkers.xml.XSLTWorker workflow java.lang.String true proteinDiseaseOutput 0 text/plain java.lang.String true drugTargetOutput 0 text/plain java.lang.String true cytoscape 0 text/plain java.lang.String true atc 0 text/plain java.lang.String true event 0 text/plain java.lang.String true fail 0 text/plain 0 EUADR_resultGraph 0 UserNameHere 2011-03-15 17:19:27.826 CET UserNameHere 2011-01-07 15:19:59.88 CET UserNameHere 2011-02-09 18:20:18.750 CET UserNameHere 2011-01-07 13:00:00.84 CET UserNameHere 2011-02-09 18:18:35.500 CET UserNameHere 2011-01-07 12:35:20.444 CET UserNameHere 2011-01-04 17:35:25.767 CET UserNameHere 2011-02-09 18:02:11.796 CET UserNameHere 2011-01-10 14:35:06.569 CET UserNameHere 2011-02-09 17:38:06.273 CET UserNameHere 2011-01-07 12:32:23.168 CET UserNameHere 2011-01-07 13:11:13.115 CET UserNameHere 2011-01-07 13:15:44.385 CET UserNameHere 2011-02-08 16:51:30.303 CET UserNameHere 2011-01-10 10:27:03.462 CET UserNameHere 2011-01-07 13:13:55.151 CET UserNameHere 2011-03-15 17:20:56.270 CET UserNameHere 2011-02-09 18:05:17.234 CET UserNameHere 2011-02-09 17:48:12.734 CET UserNameHere 2011-02-09 18:14:39.734 CET UserNameHere 2011-02-10 10:22:36.353 CET UserNameHere 2011-03-15 16:01:16.314 CET UserNameHere 2011-01-04 17:42:55.522 CET UserNameHere 2011-01-07 13:11:29.19 CET UserNameHere 2011-01-07 10:59:55.696 CET UserNameHere 2011-02-09 18:13:29.531 CET UserNameHere 2011-01-10 12:48:57.256 CET UserNameHere 2011-01-07 13:02:47.919 CET UserNameHere 2011-02-09 18:08:07.46 CET UserNameHere 2011-02-09 18:30:56.187 CET UserNameHere 2011-02-10 10:24:41.228 CET UserNameHere 2011-02-09 18:28:03.765 CET UserNameHere 2011-02-09 17:51:53.921 CET UserNameHere 2011-02-09 17:15:13.402 CET UserNameHere 2011-02-09 11:10:10.350 CET UserNameHere 2011-02-09 17:55:16.203 CET UserNameHere 2011-01-24 14:12:31.876 CET UserNameHere 2011-02-09 18:35:54.265 CET UserNameHere 2011-02-10 10:28:36.81 CET UserNameHere 2011-02-10 10:20:47.133 CET UserNameHere 2011-01-07 11:06:39.488 CET UserNameHere 2011-01-07 17:03:53.968 CET UserNameHere 2011-01-04 17:28:55.745 CET UserNameHere 2011-02-09 17:57:41.578 CET UserNameHere 2011-01-10 12:42:11.271 CET UserNameHere 2011-02-10 10:26:06.861 CET UserNameHere 2011-01-07 15:23:03.842 CET UserNameHere 2011-02-09 18:32:22.562 CET UserNameHere 2011-03-15 15:52:35.766 CET UserNameHere 2011-01-07 10:59:16.782 CET UserNameHere 2011-01-21 14:43:38.627 CET UserNameHere 2011-02-09 17:53:13.531 CET UserNameHere 2011-01-24 14:12:54.675 CET UserNameHere 2011-01-07 12:59:20.325 CET UserNameHere 2011-02-09 17:47:56.968 CET UserNameHere 2011-02-09 17:59:21.937 CET UserNameHere 2011-01-04 17:41:26.968 CET UserNameHere 2011-02-09 17:34:19.484 CET UserNameHere 2011-01-07 12:39:33.114 CET UserNameHere 2011-02-09 18:04:20.718 CET UserNameHere 2011-01-07 15:28:56.549 CET UserNameHere 2011-02-09 17:50:34.312 CET UserNameHere 2011-01-07 11:00:56.265 CET UserNameHere 2011-01-07 11:05:44.551 CET UserNameHere 2011-01-07 17:01:44.948 CET UserNameHere 2011-01-07 11:04:06.140 CET UserNameHere 2011-02-09 18:34:05.937 CET UserNameHere 2011-02-09 17:56:21.375 CET UserNameHere 2011-02-09 18:10:25.781 CET UserNameHere 2011-01-07 13:08:28.15 CET UserNameHere 2011-02-08 15:42:36.568 CET UserNameHere 2011-02-09 18:09:37.359 CET net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 2 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeXQuery_getStatusvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.2net.sf.taverna.t2.activities.stringconstant.StringConstantActivity //ns1:creator/ns1:status net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeWarningStatusgetSmileFromATCStatus0getUniProtFromSmileStatus0getDiseaseProteinsStatus0fail00answer00net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity net.sourceforge.taverna.scuflworkers.ui.WarnWorker workflow java.lang.String true getSmileFromATCStatus 0 'text/plain' java.lang.String true getUniProtFromSmileStatus 0 text/plain java.lang.String true getDiseaseProteinsStatus 0 text/plain 0 answer 0 0 fail 0 UserNameHere 2011-03-15 16:20:50.578 CET UserNameHere 2011-01-24 15:18:27.628 CET UserNameHere 2011-01-13 14:20:02.633 CET UserNameHere 2011-03-15 14:57:53.97 CET UserNameHere 2011-01-13 14:11:15.873 CET UserNameHere 2011-01-24 15:21:48.319 CET UserNameHere 2011-01-24 15:25:37.445 CET UserNameHere 2011-02-08 15:47:20.243 CET UserNameHere 2011-03-15 15:35:57.530 CET UserNameHere 2011-03-15 17:03:26.511 CET UserNameHere 2011-02-08 16:57:01.480 CET UserNameHere 2011-03-15 15:20:34.83 CET UserNameHere 2011-02-08 17:01:11.345 CET UserNameHere 2011-03-15 15:24:43.248 CET UserNameHere 2011-01-13 14:27:28.632 CET UserNameHere 2011-03-15 14:59:11.164 CET net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeXQuery_getTargetsvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.2net.sf.taverna.t2.activities.stringconstant.StringConstantActivity //ns1:targetId/code net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetDiseaseAssociatedProteinsevent0associatedProteins00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.WSDLActivity http://ibi.imim.es/axis2/services/AdrPathService?wsdl getDiseaseAssociatedProteins net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeXPath_checkStatus1xpath0xml-text0nodelistAsXML11net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker dom4j:dom4j:1.6 workflow dom4j dom4j 1.6 716010169 java.lang.String true xpath 0 'text/plain' java.lang.String true xml-text 0 'text/xml' 1 nodelist 1 l('text/plain') 1 nodelistAsXML 1 l('text/plain') net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeXPath_checkStatus2xpath0xml-text0nodelistAsXML11net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker dom4j:dom4j:1.6 workflow dom4j dom4j 1.6 716010169 java.lang.String true xpath 0 'text/plain' java.lang.String true xml-text 0 'text/xml' 1 nodelist 1 l('text/plain') 1 nodelistAsXML 1 l('text/plain') net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeXPath_checkStatus3xpath0xml-text0nodelistAsXML11net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker dom4j:dom4j:1.6 workflow dom4j dom4j 1.6 716010169 java.lang.String true xpath 0 'text/plain' java.lang.String true xml-text 0 'text/xml' 1 nodelist 1 l('text/plain') 1 nodelistAsXML 1 l('text/plain') net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetSmileFromATC_atcsource0name0code0output00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="databaseId" name="atc" qname="{http://service.alert.cgl.imim.es/xsd}databaseId"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="source" qname="databaseId&gt;source" /><s:basetype optional="true" unbounded="false" typename="string" name="code" qname="databaseId&gt;code" /><s:basetype optional="true" unbounded="false" typename="string" name="name" qname="databaseId&gt;name" /></s:elements></s:complextype></s:extensions> false source 0 'text/plain' false code 0 'text/plain' false name 0 'text/plain' 0 output 0 'text/xml' net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesource_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.2net.sf.taverna.t2.activities.stringconstant.StringConstantActivity ATC net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokename_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.2net.sf.taverna.t2.activities.stringconstant.StringConstantActivity net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetDiseaseAssociatedProteins_eventsource0code0name0output00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="databaseId" name="event" qname="{http://service.adrPath.ibi.imim.es/xsd}databaseId"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="source" qname="databaseId&gt;source" /><s:basetype optional="true" unbounded="false" typename="string" name="code" qname="databaseId&gt;code" /><s:basetype optional="true" unbounded="false" typename="string" name="name" qname="databaseId&gt;name" /></s:elements></s:complextype></s:extensions> false source 0 'text/plain' false code 0 'text/plain' false name 0 'text/plain' 0 output 0 'text/xml' net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeMerge_Liststringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.StringListMerge workflow java.lang.String true stringlist 1 l('text/plain') 0 concatenated 0 UserNameHere 2011-03-15 17:47:57.643 CET UserNameHere 2011-03-16 11:15:42.370 CET UserNameHere 2011-03-16 11:26:02.906 CET net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeTellResultmessage0title0net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity net.sourceforge.taverna.scuflworkers.ui.TellWorker workflow java.lang.String true title 0 'text/plain' java.lang.String true message 0 'text/plain' 0 answer 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoketitle_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.2net.sf.taverna.t2.activities.stringconstant.StringConstantActivity Drug-event connection through proteins net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeMerge_DPstringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.StringListMerge workflow java.lang.String true stringlist 1 l('text/plain') java.lang.String true seperator 0 'text/plain' 0 concatenated 0 UserNameHere 2011-03-15 15:54:05.439 CET UserNameHere 2011-03-15 16:02:13.906 CET UserNameHere 2011-03-15 16:02:34.395 CET UserNameHere 2011-02-10 10:47:33.906 CET net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeMerge_DTstringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.StringListMerge workflow java.lang.String true stringlist 1 l('text/plain') java.lang.String true seperator 0 'text/plain' 0 concatenated 0 UserNameHere 2011-03-15 16:17:54.276 CET UserNameHere 2011-02-10 10:47:33.906 CET UserNameHere 2011-03-15 15:57:24.932 CET UserNameHere 2011-03-15 16:03:16.76 CET net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_Listinputlist3output00net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.FlattenList workflow [B true inputlist 3 l(l('')) 0 output 0 UserNameHere 2011-03-16 11:16:23.303 CET UserNameHere 2011-03-16 11:25:06.390 CET UserNameHere 2011-03-16 11:19:08.115 CET UserNameHere 2011-03-16 11:11:10.76 CET UserNameHere 2011-03-16 11:20:19.576 CET UserNameHere 2011-03-16 11:30:35.918 CET net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetSmileFromATCatcgetSmileFromATC_atcoutputgetUniprotListFromSmilesmilegetSmileFromATCsmileXPath_getDrugTargetsxml-textgetUniprotListFromSmilerelationlistXPath_getDrugTargetsxpathXQuery_getTargetsvalueXPath_getDiseaseProteinsxpathXQuery_getTargetsvalueXPath_getDiseaseProteinsxml-textgetDiseaseAssociatedProteinsassociatedProteinsIntersectionlist2Remove_Duplicate_DTstrippedlistIntersectionlist1Remove_Duplicates_DPstrippedlistCheckConnectingProteinsintersectionListIntersectionintersectionCheckConnectingProteinsfailWarningStatusfailCheckConnectingProteinstextWarningStatusanswerRemove_Duplicate_DTstringlistXPath_getDrugTargetsnodelistAsXMLRemove_Duplicates_DPstringlistXPath_getDiseaseProteinsnodelistAsXMLConvertToCytoscapeGraphdrugTargetOutputgetUniprotListFromSmilerelationlistConvertToCytoscapeGraphcytoscapecytoscapeConvertToCytoscapeGraphatcatcConvertToCytoscapeGrapheventeventNameConvertToCytoscapeGraphproteinDiseaseOutputgetDiseaseAssociatedProteinsassociatedProteinsConvertToCytoscapeGraphfailWarningStatusfailWarningStatusgetSmileFromATCStatusXPath_checkStatus1nodelistAsXMLWarningStatusgetUniProtFromSmileStatusXPath_checkStatus2nodelistAsXMLWarningStatusgetDiseaseProteinsStatusXPath_checkStatus3nodelistAsXMLgetDiseaseAssociatedProteinseventgetDiseaseAssociatedProteins_eventoutputXPath_checkStatus1xpathXQuery_getStatusvalueXPath_checkStatus1xml-textgetSmileFromATCsmileXPath_checkStatus2xpathXQuery_getStatusvalueXPath_checkStatus2xml-textgetUniprotListFromSmilerelationlistXPath_checkStatus3xpathXQuery_getStatusvalueXPath_checkStatus3xml-textgetDiseaseAssociatedProteinsassociatedProteinsgetSmileFromATC_atcsourcesource_valuevaluegetSmileFromATC_atcnamename_valuevaluegetSmileFromATC_atccodeatcgetDiseaseAssociatedProteins_eventsourceeventTypegetDiseaseAssociatedProteins_eventcodeeventgetDiseaseAssociatedProteins_eventnameeventNameMerge_ListstringlistIntersectionintersectionTellResultmessageCheckConnectingProteinsresultTellResulttitletitle_valuevalueMerge_DPstringlistRemove_Duplicates_DPstrippedlistMerge_DTstringlistRemove_Duplicate_DTstrippedlistFlatten_ListinputlistConvertToCytoscapeGraphEUADR_resultGraphdiseaseProteinsOutputgetDiseaseAssociatedProteinsassociatedProteinsdrugTargetsOutputgetUniprotListFromSmilerelationlistconnectingProteinsMerge_ListconcatenatedCytoscapeResultGraphFlatten_ListoutputdiseaseProteinsMerge_DPconcatenateddrugTargetsMerge_DTconcatenated 6ebbf226-8fb0-4091-94d2-b1e847660440 2011-02-09 17:48:16.625 CET 5014d953-b1a6-4be6-82ca-989681510645 2011-01-14 18:31:49.315 CET 984a9292-80d5-4a03-bf77-cec858d566b3 2011-01-04 17:45:55.665 CET EUADR IBI-CGL signal substantiation through proteins 2011-02-08 18:00:32.122 CET ddc6814a-cbf4-4dda-a811-c62cac125370 2011-02-09 17:38:26.900 CET 1b852c51-9908-46b1-b68c-3f169682f23e 2011-01-17 12:09:55.130 CET 93d045f8-5566-400e-b931-2aca1f9b3947 2011-01-13 16:28:44.447 CET 2f799556-78fe-4d91-a0b9-989191ba3703 2011-01-13 16:39:50.188 CET 62ec5abb-7c12-4bb9-af57-456cbcbbda9e 2011-01-10 12:42:16.19 CET f62bd8c1-d09f-44de-b891-2c79ae117468 2011-03-15 17:15:21.271 CET de0177bc-8afe-45a1-8529-745eb94492ae 2011-02-08 17:02:47.966 CET d471959c-29f3-49f6-bda2-5eaec8dd5ea8 2011-01-17 11:45:21.958 CET b54625a7-01c7-451c-9c07-2e97ae8ba326 2011-01-04 12:57:37.762 CET 3283fbbf-0535-4a4f-a865-8d4a46e02994 2011-02-09 17:38:10.996 CET 651ca0ac-273a-4389-af28-84ce7367b451 2011-03-15 17:42:28.239 CET 6ec2cc26-423a-42f7-ac27-a9e7c87bdaf5 2011-02-09 17:23:41.748 CET 7ff8652c-45ab-446f-b865-79c80d90880a 2011-01-17 14:06:06.709 CET cad732c9-8359-465b-ba8c-b93fd44bfa54 2011-01-13 16:49:14.442 CET cc772697-d010-4057-b756-36c08166d645 2011-01-17 10:35:59.185 CET 6e2b4cbf-362f-458c-901a-9fd1be0c6a59 2011-03-16 11:16:28.606 CET 62c3de99-9361-480c-ade0-4c3c3c7b54d1 2011-02-10 10:53:41.501 CET 69676201-0660-4b18-9e0f-5f103d467523 2011-01-13 16:31:34.241 CET c6d50660-c118-4896-8133-479b21f168b1 2010-09-30 18:06:34.340 CEST 58589cdb-d8d6-45a3-83c5-116afa1f09d3 2011-01-17 14:03:03.793 CET 53503b95-945b-46d3-8663-5b176536f52c 2011-01-04 15:52:11.52 CET af689045-45d3-4ca2-9e63-d833cdfd4803 2011-01-20 15:23:08.969 CET 656f5a21-7dc4-4e46-a6e4-67fd197decfe 2011-01-14 18:08:30.745 CET 1bcb72f3-d887-46db-8987-5110137dee7c 2011-01-13 16:56:08.617 CET 0db3f322-5f1f-4505-bf6a-85c5a9eeb289 2011-01-04 12:48:54.533 CET 44ef6149-c0e2-4466-90b2-f13051fbe7ca 2011-01-13 15:49:08.268 CET 843affcb-828f-4624-852b-a2e99dda68ea 2011-01-04 16:06:49.11 CET 240b6e21-4a2b-4864-9fe4-24617da3c923 2011-02-09 18:09:40.562 CET 09b3d4f2-ac6b-49de-bc63-c4fc83379834 2010-09-08 15:39:11.360 CEST 4e6551ac-5a84-4458-9c20-554bcf8f6af9 2011-02-09 18:10:29.46 CET a902b378-4626-4df8-809a-93123c33c9a9 2011-01-04 12:15:24.2 CET d19909e8-669b-4d65-9468-f760fd7fa750 2011-01-07 17:04:00.846 CET 7b7bf9ce-5249-4ad0-af27-ef7987d5c051 2011-01-07 11:01:45.884 CET a44786bf-7821-4d57-b90b-5f54ea6fed27 2011-01-07 13:15:50.669 CET 6ec9aa19-abe1-42de-a705-323f80a67131 2011-03-16 11:16:51.196 CET a59a2bab-0fc2-42fc-a036-3c11c376ec33 2011-01-24 14:13:23.143 CET ADR_substantiation_through_proteins 2011-03-03 17:26:30.535 CET a76a5bbb-91e9-4b5b-b371-83adbb3c2f00 2011-01-13 15:56:40.508 CET 6953c726-0841-4a21-b77e-e7f6c2ca6dbc 2011-02-10 10:21:11.613 CET 653e4e25-055c-4379-9a83-2d1151d8478a 2011-01-14 18:14:09.85 CET f487558d-5599-490a-9c57-8eeb3f9537ac 2010-09-30 18:11:10.559 CEST 9aa3115d-bd94-4143-9527-a47bdbda1c3e 2010-09-08 17:07:48.587 CEST 8038ad73-2341-401f-9a99-1c9f30862a90 2011-01-07 11:04:15.227 CET d5bc6c59-70e8-43fe-9212-191b0040b888 2011-01-04 11:45:28.859 CET f331ed5c-0969-4bb7-8888-69b3eccf80f9 2011-01-10 14:35:40.987 CET 23016ee1-4112-467f-8d95-7a0fccec501d 2011-01-13 15:52:05.450 CET b80fba38-d085-4bef-924a-417825107648 2011-01-04 15:49:32.364 CET f9b47244-65d6-4589-8718-b5e33ef485bd 2011-01-13 16:38:20.39 CET cbb45c11-e394-4e86-8c64-ccd5ddac1557 2011-03-15 16:58:40.666 CET 04372b6f-fcc3-4b2c-83ac-b64512f59ce2 2010-09-17 10:39:50.849 CEST 20f2f5df-9b73-4c47-b553-b87ed68e7089 2011-02-10 10:47:58.865 CET b7af5884-8ad6-4201-a2b5-6d7a2d6160ad 2010-09-08 15:45:03.444 CEST 33ba9d75-43b9-40e6-a927-a2405aed31db 2011-02-08 16:51:34.505 CET dd6c4837-c654-4f83-912e-d46922e0e0a0 2010-09-08 17:08:39.265 CEST a806ad18-4400-4a05-892d-60824552fb1d 2011-03-16 11:26:10.901 CET 5c5101bf-6e14-400c-bcd6-66a7b4f6094b 2011-01-19 17:33:29.326 CET fc739216-5572-42da-b597-25164e559ad8 2011-03-16 11:30:48.20 CET 252516db-cfe7-46d5-9881-9dec832ee325 2011-02-08 15:59:28.584 CET f59f4c3a-a7d6-4df8-bf54-20cd54c95bad 2011-01-04 13:53:35.962 CET 8eccba26-6a75-488f-a99e-e73d57d7b601 2011-01-05 17:56:23.509 CET be65a81f-1248-489e-8568-c4a852d6824f 2011-02-08 15:48:18.768 CET b66fe7cc-39dc-4949-afc0-83c195751d59 2011-01-04 17:36:27.395 CET 5f5a4dee-045f-4720-b990-9445ce4ce627 2010-09-30 18:03:28.544 CEST fc036ee8-4923-46c9-ab97-48fd1d0edba4 2011-01-04 17:35:51.643 CET Anna Bauer-Mehren Integrative Biomedical Informatics Laboratory (GRIB, IMIM/UPF) 2011-02-08 15:52:33.136 CET f2f5f285-9c68-4a07-a77e-ffc3995a8738 2011-01-04 13:44:31.852 CET abbe5ecd-c5c5-461f-9b16-860c7f8e6a17 2011-03-15 17:03:34.308 CET e57ad22d-32f9-4fc7-80d1-9186a849119b 2011-01-07 15:27:40.662 CET 37da3e95-eeed-450f-bf0a-9037a652e500 2011-01-24 17:29:39.214 CET af060e60-6938-4295-8797-8c749b8d4085 2011-01-14 18:04:03.419 CET 76842ae5-75ab-40b2-a41a-c819c08de42a 2011-02-09 17:59:28.250 CET Anna Bauer-Mehren 2010-07-19 13:20:18.173 CEST 2fff42ee-f6f2-418e-8497-fd251d8aaf7d 2011-01-10 12:53:40.490 CET ab8a5018-e8a5-4518-8568-af60ea5aa611 2011-01-24 15:17:23.110 CET 77ccfaf3-08a2-49da-812d-c02cca424c89 2011-03-15 15:24:47.4 CET Anna Bauer-Mehren Integrative Biomedical Informatics Laboratory (GRIB, IMIM/UPF), Barcelona, Spain 2011-03-03 17:27:24.897 CET 24cb7be8-e08f-4491-8bf8-35b00b118495 2010-08-26 16:41:14.887 CEST ce90a78b-213d-4780-b28e-45585adcfd4c 2011-02-10 10:23:45.17 CET a4c22227-00af-4525-bd90-2741da71a846 2010-09-30 17:59:44.739 CEST 8d0c6e40-d3b7-4e40-9c18-b7ced289aaa3 2011-02-09 18:18:39.484 CET 3f105056-fcab-4bc4-8cf8-9951729b24df 2011-01-04 12:17:29.826 CET e5acb382-1cf9-4792-ab8f-ba1ad87eef82 2011-01-04 14:04:01.351 CET 15493c2e-a54c-493e-8898-710705b8c5d7 2010-09-08 16:38:16.856 CEST 43b3cf7d-34d8-49d6-9eae-19e8a5d41cc1 2011-03-15 16:18:53.106 CET d59db508-04af-4d13-b5c6-5523ff815d7a 2011-03-15 17:37:45.624 CET c92f43ec-b8a5-4238-bbba-c7e950131b3f 2011-02-09 18:28:07.843 CET 7aa10c7d-6fe1-4b77-8808-7cffa61ae3db 2010-09-14 15:35:08.242 CEST ed4d02f5-5289-42ac-aa18-6939e670363b 2011-01-07 11:05:51.928 CET cb84c608-6105-4b6b-9bb7-77acb56389ed 2010-09-17 10:52:24.545 CEST ae92fb5d-fd57-4faa-ba70-55607ed78347 2011-01-17 12:38:05.300 CET 501fec94-9965-4157-b32e-867a106712f3 2011-01-14 18:22:44.494 CET cc3023d1-fed7-4870-8dd9-467cea4c01fe 2010-09-08 15:29:14.947 CEST 2720a061-814b-4cf5-9d49-653a1c738e37 2010-07-29 09:51:48.234 CEST d46cd2df-d9a7-4508-9364-bc45cbe8158e 2011-01-13 16:20:17.110 CET 06b488ab-b4b6-4fdf-bf4e-557d1d5b0d2c 2011-01-04 16:21:31.258 CET 2f0b90b4-41c1-4675-bbbb-37ee904f88b4 2011-01-14 18:10:30.484 CET 2a0e987e-189e-485c-9a44-b13fb379d459 2010-12-21 15:44:16.508 CET Anna 2010-07-19 13:20:04.607 CEST This workflow substantiates drug safety signals which are composed of a drug and an adverse reaction. In more detail, it checks if there are proteins that are annotated to a given adverse event and at the same time target of the given drug. As adverse event, the following event types are allowed: 1) events as defined in the EU-ADR project such as UGIB 2) UMLS CUI concept identifiers As drug input 7 digit drug ATC codes are allowed. As result a list of intersecting proteins is provided. If this list is not empty, the drug-event pair is substantiated as signal. Moreover, a Cytoscape graph is generated for user-friendly visualization. It contains the event, drug and their annotated proteins as well as additional information such as links to publications etc. 2011-03-03 17:27:12.912 CET 8605e865-958b-4f8e-834e-2806d9b1582e 2011-01-07 11:06:46.487 CET 3b5e0702-3362-4022-9f9b-453acf20494e 2011-01-04 16:10:11.817 CET 5b69bd99-3672-45f0-9518-c0186ea88345 2011-01-25 09:30:05.429 CET b395013e-3879-47e8-822a-18a8a2d43149 2011-01-04 17:41:43.118 CET 39610a7c-e061-4f9d-bd80-88309bbd6ab9 2011-01-17 11:32:10.27 CET 9fe4accf-0799-41bc-b67c-83a641e8311f 2011-01-10 12:46:26.160 CET 076569ba-ad9a-4ba8-8f8e-66c56972887c 2011-03-15 17:00:19.815 CET 0ea7d095-fc78-475b-9a96-efc6e41811dc 2011-01-04 15:43:14.845 CET 40464dda-dfeb-4f4d-ad59-8d6800af40bd 2011-02-08 17:01:17.380 CET 2f700972-4f65-4993-9d83-d66122a57548 2011-01-13 16:13:22.795 CET 935964c1-91b9-4e5f-9c32-ed5fccf9f9a2 2010-09-17 10:14:21.353 CEST 7a9a9b49-6e78-4ad0-b3e6-d63926f362b3 2011-03-15 13:33:04.772 CET 30c736d4-4c56-46cc-8612-f4c24e3e8bf4 2011-02-09 18:13:35.828 CET 37d45e5b-c0ef-4f73-9a69-9b1048f8cc67 2011-01-13 14:01:08.590 CET f2c45435-2f63-4179-879b-323954bcd773 2011-01-17 12:51:01.494 CET 1897606e-1d7d-4c96-ab38-6ef1b9cf38ac 2010-09-30 18:05:13.306 CEST 9f6fca78-6d4d-4e62-90d4-2211905b83f1 2011-01-21 14:20:14.134 CET 6548e9cf-5bec-477f-96a0-6b1d8c5d082d 2011-02-08 18:26:56.320 CET bfb6d7b3-3dd3-43f4-866d-10d2d658bd9a 2010-12-22 11:59:44.908 CET cc468b4a-24fe-4463-ad13-fec4ff026441 2011-01-04 11:14:23.26 CET de97e1d3-167f-4dae-917d-197e2e4b27b3 2010-09-30 18:00:40.4 CEST 554c0775-68cf-419c-8202-2f1baa1a9dca 2011-01-04 12:04:35.852 CET a9eb117a-c4ac-4dbf-b89b-ad9f7d8411f4 2011-02-08 15:54:29.681 CET a063837a-bf23-42da-8892-eb8044555c19 2010-09-30 18:08:32.887 CEST d0f1571c-f4db-4fb7-876d-d75377402016 2011-02-09 17:56:25.750 CET fba94945-80a5-49b0-a6e3-af17dd3ef7f0 2011-02-09 17:34:29.497 CET d7824096-eb0c-4fb9-87f5-0341596b5211 2010-09-17 10:48:39.9 CEST 26f73c21-400f-4c63-8b61-ca6d410a49ca 2011-01-04 15:44:49.895 CET d927ef64-6cd0-45e8-ae2b-9ff77bc31765 2011-01-04 16:18:35.499 CET 21f344c5-c9f9-4801-af16-599fec21492b 2011-01-13 16:32:59.459 CET f13ae848-8516-4192-9e86-4aff2853694d 2011-01-07 13:02:55.763 CET 29d4ed3a-8ab6-4d17-95e3-a0f61f4c6bed 2011-04-18 17:30:34.694 CEST 8953bc2a-c768-4876-838b-b90aa79254ac 2010-09-08 16:31:59.996 CEST 6e32b8bb-01e4-4abc-a589-2577b16b8f9c 2011-01-13 16:30:25.16 CET e8d8164d-cf5a-43ae-8ca6-18becacf8d8b 2011-01-07 12:41:50.692 CET 64f4a75e-d537-42bb-85fd-895bd35969c2 2011-01-13 15:54:42.790 CET c2380230-dead-428e-b027-c0ca4ed2233f 2011-03-16 12:30:33.623 CET 69d9e94d-4948-4cf2-93ae-a6bb2cd71a8a 2010-09-08 15:30:15.132 CEST 0b1a7caa-589a-4fe2-a52c-3b0611d4abb5 2011-01-24 17:14:53.841 CET f25c3841-8afe-4c63-94be-d2d454ddbf48 2011-01-24 12:30:57.285 CET 5625eddc-85bc-4748-a9d4-fea753e8860f 2011-01-04 12:06:44.735 CET 37c313f4-fc7f-44fb-b486-75344db8f933 2011-01-13 15:50:00.475 CET d4af1b5a-8069-4f1b-8053-b93d773a4b79 2011-01-24 14:13:35.151 CET fee13559-e86b-4418-9599-f2a1d6446c75 2011-01-13 16:50:29.626 CET 7fc58eec-fb7e-4719-951c-f8c7402bdbdd 2011-02-09 18:20:22.593 CET 2b00853f-d2b9-4986-8085-fc3de81a7693 2010-09-08 17:25:02.20 CEST 53931c4d-2c75-4148-acde-8f69bb7fd626 2011-01-14 18:03:03.413 CET ff1f9074-7f1b-4f04-b09b-25e8d1075933 2011-01-17 11:08:52.797 CET f6450ab7-d5fe-4ae5-b7f0-36f7a29cb8b4 2011-01-04 12:52:56.78 CET cf360835-3b60-421b-a4a3-ff67fffa4aaf 2011-01-17 11:24:32.777 CET 0ed622c5-32b6-4791-be7a-382da065f086 2010-12-20 16:03:47.872 CET 776ad2f6-e9ba-4c99-ad3a-772b5e9cb61b 2010-12-21 15:39:22.876 CET EU-ADR IBI-CGL signal substantiation through proteins 2011-02-08 15:48:19.784 CET a7637da4-1853-47eb-b6b6-6b6187de4968 2010-09-08 15:37:34.78 CEST 5ff684db-0eed-4796-8dc5-517f213b56a2 2011-01-10 10:27:14.753 CET 78c2ffad-6362-4ab3-b4b7-934b210ef48b 2010-12-20 15:33:23.98 CET 68aa3ee9-2188-46fe-b328-58cb9ffcef61 2011-03-16 11:12:34.645 CET bdcb966c-e208-4f2b-9e51-507e2da5a378 2011-03-03 17:27:27.737 CET 32656a2e-ee50-4835-b479-aabc4396016f 2011-01-04 13:57:15.461 CET dd725567-2a4d-4685-9f8c-9722acf4d225 2011-03-15 17:31:44.488 CET d42fa9b2-722c-4842-b57a-d66e98a65156 2011-01-17 12:36:51.706 CET bf84dfe6-5cbe-488b-86e4-4a71ece58e69 2010-09-08 15:35:53.307 CEST 5a385bf1-6932-4e41-80f9-e06dd644f32c 2011-07-29 17:38:38.740 CEST 40c5876a-1731-454a-8463-a1bc4746279e 2011-02-09 18:32:24.812 CET 7c0b2875-054e-40a4-a02e-1135e93e9084 2011-03-16 11:21:50.99 CET 11a2dca5-f9cc-4121-ac2d-1da011bf6ad8 2011-01-04 16:15:49.408 CET c8575cda-c374-412c-8a5a-217362c83ffd 2011-03-15 17:33:58.694 CET 2fe89980-66f4-4bea-9c9e-c28ef4ea10ac 2011-01-24 17:10:29.201 CET 4f339317-dc4d-4151-8203-893f0e707b07 2011-01-07 15:23:18.432 CET 88f6405e-9afb-4f26-9a78-36c60e5a4dcd 2011-01-17 12:32:11.716 CET a75d9a51-eff5-406c-87e4-9b819a305c0b 2011-01-04 11:19:54.815 CET b38d4ffb-21bf-4544-973d-bb152f843312 2011-02-09 17:57:43.937 CET 7dcbaabc-a79e-4438-8203-cfd54c97445f 2011-01-21 14:43:56.580 CET 7bdae3e8-a90c-434a-b7d9-a0479072e7cb 2011-02-08 15:47:42.312 CET 5022eb2d-6711-4b4b-97e0-8c62f9776c45 2011-01-07 13:03:46.867 CET 658773b8-c856-4e48-a0b8-50e41be3d69d 2010-12-20 15:49:39.984 CET ca5a4b71-527c-4651-acb1-a99f7f6ba08a 2011-02-09 18:04:27.312 CET 432f00f4-ba45-4877-b237-7352e0217da0 2011-03-15 13:37:09.657 CET EU-ADR IMIM 2010-07-19 13:20:24.541 CEST 5407a926-aa31-4f07-a813-f44a9655c734 2011-02-09 18:35:59.593 CET This workflow checks if there are proteins that are annotated to a given adverse event and at the same time target of the given drug. As adverse event, the following event types are allowed: 1) events as defined in the EU-ADR project such as UGIB 2) UMLS CUI concept identifiers As drug input 7 digit drug ATC codes are allowed. As result a list of intersecting proteins is provided. If this list is not empty, the drug-event pair is substantiated as signal. Moreover, a Cytoscape graph is generated for user-friendly visualization. It contains the event, drug and their annotated proteins as well as additional information such as links to publications etc. 2011-02-08 15:51:53.365 CET f2ce956e-e544-4d6c-a04f-534d59886d87 2011-02-08 16:00:52.362 CET 048a6d98-ed9c-4cd8-bee7-4dc5f1f46c01 2011-02-08 18:27:28.1 CET 29997a06-3ae7-417d-802d-241052e0e37e 2011-02-09 17:53:18.656 CET 8c38e822-a0f2-410e-85ee-91323183e0e0 2011-01-24 17:15:33.722 CET a57e7167-8c78-44a8-ae42-46497cef3946 2011-02-08 15:55:16.626 CET ee4f5456-69c2-41e9-af9d-94e919a4f01a 2011-01-14 18:13:16.336 CET 131d2a55-29eb-4e0b-9fbd-8a4a5d6eea27 2011-02-08 17:05:26.693 CET 72861079-56e6-4799-8d89-c3ef3936d0e9 2011-02-08 15:47:24.63 CET df58c7fa-b2a2-47e8-812d-11219ce48b55 2011-03-16 12:08:28.954 CET 72609134-3363-4249-8add-e09874606101 2011-01-07 13:00:06.54 CET cba4e9b3-6dcb-4e2f-9ebe-08f42ed5bc38 2011-01-17 12:49:37.448 CET 882c06d0-a11e-4967-a338-a8c67dfa4fb4 2010-08-26 19:22:46.869 CEST f5f7d39a-e76c-4988-88a4-7d9e61f3b116 2011-01-04 12:59:27.437 CET b3d4faab-9dfa-45b5-a855-af8fe03235e6 2011-03-16 11:15:47.889 CET 218c5dcc-3492-4ba4-a473-9264f389058b 2011-01-17 12:43:10.315 CET 04e3fe6e-03c9-477b-a266-3d01e1631396 2011-02-08 18:28:27.370 CET 16d25054-8d45-4fe1-b67e-8266e8682415 2011-03-15 17:19:39.625 CET ee350468-e12d-48cb-9483-4e9acd0509af 2011-02-09 17:50:36.890 CET 9ad59fb2-c2bd-4f4d-a40f-688ee37a56da 2011-03-15 13:36:09.912 CET 26f00868-c8de-4c53-9986-9a81ee18dd5c 2011-03-15 17:22:48.766 CET e5ff72f4-929a-47fb-8592-cae2dbbbd2e0 2011-01-14 18:29:12.87 CET 4183fd75-868c-4209-9b1f-1a6983402288 2010-09-17 10:44:54.881 CEST 8b7cf829-7859-420c-b9c8-01f98b083d36 2011-01-13 14:32:57.871 CET 1a2c2f66-f7a9-4fa5-b132-c1583063a454 2011-02-10 10:26:14.42 CET b0ee9766-858e-46f7-a2cb-d38178b66a24 2011-01-13 14:29:33.126 CET 0095e0ec-82cd-49ab-9e01-60bdd3817224 2011-01-24 15:32:15.832 CET 1354b590-e1d4-4a80-a3b6-b0443bb0269d 2011-02-08 15:52:32.206 CET 7a9c8a93-8d29-4381-8c04-60150fbed445 2011-02-10 10:28:46.36 CET 85a3ae41-67b5-45fa-820d-912538444b1a 2011-01-13 12:45:21.974 CET 2362930f-4165-4040-ae48-972079c15b99 2011-01-04 14:00:35.449 CET a8565d7f-1947-49e1-9370-015e1f93b603 2011-01-07 12:32:28.763 CET 1dfeeb2f-41ee-445d-b780-38367b4bcc78 2010-09-30 17:58:44.713 CEST e98d765a-4eec-4f87-b05f-04c5591efc9a 2011-01-07 11:01:18.944 CET fddb1035-bbbc-4bf5-bef4-17698d5fc163 2011-01-24 17:17:23.149 CET cc8f4d14-0ace-4cc8-8fff-f96b78239046 2010-09-17 10:14:44.745 CEST eef744ef-73f2-46c4-a707-9dde6e6989ae 2011-01-24 15:28:34.452 CET ea3c8053-5bbe-4e33-bd69-2959d54efd11 2011-01-13 16:18:36.312 CET 9685469c-cba1-4b00-a143-e3da2cc2c9e9 2011-02-09 18:02:13.953 CET fa61c748-de3c-4438-ad8a-33dd39fcb76f 2011-01-04 13:59:46.545 CET 3edb1d6f-00b2-45d6-94f9-c5b99d15f2eb 2010-09-17 10:53:44.129 CEST a12cecc7-2962-4b13-89d5-3b60eaf69648 2011-01-04 12:56:07.950 CET 7aee53f2-268c-416f-ad06-55a0fd9ac22e 2011-02-10 10:18:24.247 CET 9d1b78c8-5d43-43cd-9e41-2c0d26290119 2011-01-17 10:57:16.237 CET 5b108f21-e22f-4d6c-b3a2-280552f43296 2011-01-13 16:16:16.29 CET 7a29253f-18a9-4d66-bc12-b0ba27158309 2011-01-10 12:49:12.709 CET 96b888b5-0878-4702-84d0-447e7907feec 2011-01-04 16:34:24.129 CET a59568bd-3909-4380-a924-be18570272b5 2011-01-04 13:46:26.232 CET f941ca21-1633-4f04-81ef-b9ba74c78a34 2011-01-10 14:36:36.252 CET 26684f01-4aa0-4978-a550-e05136d111e4 2011-02-09 18:08:11.625 CET d96151a8-8ca1-4d81-9cb8-ecc16e5c5d89 2011-02-08 18:34:46.650 CET 497d97fc-2cb4-499c-a839-51809a6b4654 2011-01-19 17:30:01.794 CET f9e948ad-30a4-424c-8ab7-63452decf4e0 2011-02-09 18:05:20.171 CET f9662ff3-5ad3-42ec-8930-68c628fd6502 2010-09-17 10:42:02.441 CEST 4374f1b9-35c3-4a9d-a2f8-c3132d786738 2011-03-15 17:18:28.925 CET ec1e578a-6980-4a25-8a64-471a590d70c4 2011-01-07 13:22:32.167 CET b8238866-091e-4bfd-8b53-3169af5e67ae 2011-01-04 12:09:27.450 CET 43441d50-4ecb-40e5-9185-36ef40441472 2011-03-15 17:53:53.247 CET d9244dcd-5e77-49c5-bd98-5778ffcbf7a1 2011-01-07 15:29:00.928 CET 83fa5a60-5dd9-47d5-b2bc-5e17c2e0d787 2011-02-10 10:25:03.370 CET 87ce4583-2a1f-477c-9c17-9253f6bf35b9 2010-09-14 15:33:56.170 CEST 42b2ed0c-0986-4653-b953-a0514a4849d0 2011-01-24 15:29:05.764 CET 667271d2-597d-4625-91ce-d075886b89de 2011-01-04 13:51:48.724 CET 6027b3fe-852f-425c-ae29-e863b1661433 2010-09-08 15:33:59.145 CEST bce8d803-d64b-434f-af97-31aebc72300a 2011-01-14 18:06:06.550 CET 4c996435-c3af-4457-a92a-fbc7fd30b8e5 2011-02-09 11:10:34.38 CET b87d929c-35cb-42b2-9b85-5da55b571720 2011-01-17 11:43:19.215 CET 2fc970ff-568d-4991-b44b-cf3081b98a50 2011-01-14 18:12:06.86 CET 0c4617d8-938b-497a-bd9b-e24a88881333 2010-09-17 10:49:31.705 CEST 314d80ed-264b-4396-a047-2f628bea9161 2010-09-17 10:43:21.150 CEST c4308939-a661-4907-8606-1a86778d8947 2010-07-29 18:24:46.817 CEST 7d489ce0-6ed6-43d3-97fa-45fd176e818a 2010-09-30 17:57:08.458 CEST b5507185-dd64-40aa-8e17-80cc8e6e5e86 2010-09-14 15:31:11.179 CEST 841e6b3c-7b1b-4e30-a333-d4876429e1f2 2011-01-13 15:08:13.15 CET e6e7b199-0a83-4484-95dc-61dbdb82084b 2011-03-15 16:03:31.248 CET cbdfc13f-df16-4965-bc74-605d26c7d03f 2011-01-13 12:51:13.433 CET 22dcfced-3d12-4200-a000-740b980ced07 2011-03-16 16:23:42.572 CET adeabcaf-68dc-4c50-ba2d-cbe94c6819cd 2011-03-15 15:57:50.265 CET df79c8c4-6777-48c5-9d59-00ccab13e43d 2011-01-04 16:13:26.111 CET ab28e2f3-9232-420a-bcf9-13bb1f774a02 2011-02-08 15:52:34.326 CET dd12e38a-a639-4553-8fd5-fb278a79b444 2011-01-07 12:39:58.59 CET 55639062-218e-41bb-839e-d2c3d4659a1c 2010-08-26 17:15:56.889 CEST 58bbae56-adfb-44c2-9b50-0a055c655970 2011-01-17 10:38:00.451 CET d0498cc8-621b-4e2f-aa6b-87b5b47aaa46 2011-02-09 18:14:42.593 CET 0aabc0d8-a7bb-4b9b-a8aa-6d238ce4d7db 2010-08-26 19:24:05.143 CEST 193d9e9b-4196-427e-8fc0-321cbd79a24a 2011-02-08 15:42:42.20 CET 99b09bd0-fbde-4b36-a901-ddc37b71f19d 2011-03-15 15:24:00.539 CET 3d05b413-9350-46d1-afae-f1db198659c7 2010-09-17 10:40:56.793 CEST 8cd36716-c8a9-4ff0-93a9-9530dfc78bb9 2011-02-09 17:55:19.437 CET 304ef1c5-fee1-4c6d-9d22-2b0a8b3285fc 2011-01-17 12:50:25.677 CET 20505947-c57b-4bd0-8ebc-6a2fd7082695 2011-02-08 18:02:19.99 CET 5bb85af5-a496-4d13-a8e3-4dc8ed33713c 2011-03-15 15:49:27.533 CET 51b94baf-5dc4-4093-93ed-675f22842e6b 2011-03-15 17:39:39.758 CET 8e17ab19-7c07-4906-a32f-a416f706188d 2010-09-08 15:34:46.474 CEST d08bc93b-51c4-4c40-bd72-11d549c32ead 2011-01-13 14:06:02.321 CET 86ef6f43-c15f-4c2b-940a-1a73704cbaac 2011-01-10 12:49:33.152 CET 21e4c0a6-9a6c-4460-9c47-127288c8b219 2011-01-07 17:01:53.65 CET 4b08aa99-b8dc-4318-9bf3-0cf0350ab3b2 2011-01-04 17:43:08.489 CET e2c37fc0-0f67-4d25-8cbb-b37672fc6f19 2011-01-21 14:21:30.282 CET 4f80ffa7-b20d-46d2-a4dc-0c456188b0b4 2011-03-03 17:27:23.585 CET 423144e5-b1a3-44e0-a4c7-2033e1118085 2011-01-07 13:14:01.754 CET 4746b9ae-526f-48ab-b0c9-8db651c63d99 2011-03-15 15:20:36.732 CET deb58f7d-9e66-44bb-b930-e5e49ea313cb 2010-12-20 15:29:06.561 CET ec258c77-f3a3-4657-9329-c820ab6870c6 2011-01-04 12:47:28.68 CET b96f98ce-8fe3-4eb7-b6c6-79ddbab80302 2011-02-09 18:34:08.875 CET 234336e6-ed6f-423e-b2ab-f3329a87cb43 2011-03-15 14:59:32.577 CET 0bff4792-0550-4275-9469-51ab7f99b75b 2011-03-15 16:23:14.747 CET 2c032302-7b2d-456c-8535-738147b8b899 2011-02-09 17:51:57.265 CET d9173713-01e6-42cc-a1e3-cbf3ef27a6b3 2011-01-13 14:48:14.496 CET f6a9a5d5-7bc0-4e6a-a358-86323f82185f 2011-03-15 17:26:10.456 CET c37dbf69-e5ac-451a-b579-163c7ac5d665 2011-01-17 10:32:32.30 CET 41db8492-1074-4db3-a1f7-91f6e570c1e8 2011-02-08 18:28:32.994 CET