Pathway_and_Gene_to_Pubmedgene_names00text/plain2010-12-24 16:25:08.996 GMT2010-12-24 16:25:08.998 GMTPhenotype_search_term00pathway_descriptions00gene_abstractstext/plain2010-12-24 16:25:09.3 GMTphenotype_abstractsphenotype_termsphenotype_term_countspubmed_abstract_numbergene_cosinegene_term_enrichment_scorespathway_abstractspathway_cosine_vector_scorespathway_concept_rankingsregexvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity\nnet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeremove_nullsinput0output00net.sf.taverna.t2.activitiesbeanshell-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivityinput0'text/plain'java.lang.Stringtrueoutput0'text/plain'0workflownet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokegene_and_abstractabstracts0pathway0output00net.sf.taverna.t2.activitiesbeanshell-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivitypathway0'text/plain'java.lang.Stringtrueabstracts0'text/plain'java.lang.Stringtrueoutput0'text/plain'0workflownet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesplit_search_termsregex0string0split11net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivitystring0'text/plain'java.lang.Stringtrueregex0'text/plain'java.lang.Stringtruesplit1l('text/plain')1workfloworg.embl.ebi.escience.scuflworkers.java.SplitByRegexnet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemerge_outputs_2stringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivitystringlist1l('text/plain')java.lang.Stringtrueseperator0'text/plain'java.lang.Stringtrueconcatenated0'text/plain'0workfloworg.embl.ebi.escience.scuflworkers.java.StringListMergenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSearch_PubMedsearch_term0min_date0max_date0max_return0concat_data00net.sf.taverna.t2.activitiesdataflow-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize5net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050005net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeclean_textinput0cleaned_text00net.sf.taverna.t2.activitiesdataflow-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050005net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregular_expressionvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity\nnet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRemove_duplicate_genesstringlist1strippedlist11net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivitystringlist1l('text/plain')java.lang.Stringtruestrippedlist1l('text/plain')1workfloworg.embl.ebi.escience.scuflworkers.java.StringStripDuplicatesnet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesplit_gene_namesstring0regex0split11net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivitystring0'text/plain'java.lang.Stringtrueregex0'text/plain'java.lang.Stringtruesplit1l('text/plain')1workfloworg.embl.ebi.escience.scuflworkers.java.SplitByRegexnet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeremove_Nulls_2input0output00net.sf.taverna.t2.activitiesbeanshell-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivityinput0'text/plain'java.lang.Stringtrueoutput0'text/plain'0workflownet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeMerge_string_list_to_stringstringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivitystringlist1l('text/plain')java.lang.Stringtrueseperator0'text/plain'java.lang.Stringtrueconcatenated0'text/plain'0workfloworg.embl.ebi.escience.scuflworkers.java.StringListMergenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokexpathvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity/*[local-name(.)='eSearchResult']/*[local-name(.)='IdList']/*[local-name(.)='Id']net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokerun_eSearchparameters0attachmentList11parameters00net.sf.taverna.t2.activitieswsdl-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdlrun_eSearchnet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize5net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemin_datevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity2000/01/01net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeextractPMIDxpath0xml-text0nodelistAsXML11nodelist11net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivityxpath0'text/plain'java.lang.Stringtruexml-text0'text/xml'java.lang.Stringtruenodelist1l('text/plain')1nodelistAsXML1l('text/plain')1workflowdom4jdom4j1.6716010169dom4j:dom4j:1.6net.sourceforge.taverna.scuflworkers.xml.XPathTextWorkernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeremove_Nulls_4input0output00net.sf.taverna.t2.activitiesbeanshell-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivityinput0'text/plain'java.lang.Stringtrueoutput0'text/plain'0workflownet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeconcat_abstract_idsid0abstract_text0date_text0output00net.sf.taverna.t2.activitiesbeanshell-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivityid0'text/plain'java.lang.Stringtrueabstract_text0'text/plain'java.lang.Stringtruedate_text0'text/plain'java.lang.Stringtrueoutput00workflownet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemax_return_phenotypevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity5000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokepubmed_databasevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivitypubmednet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemerge_phenotype_abstractsabstracts0phenotype0output00net.sf.taverna.t2.activitiesbeanshell-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivityphenotype0'text/plain'java.lang.Stringtrueabstracts0'text/plain'java.lang.Stringtrueoutput0'text/plain'0workflownet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemerge_abstractsstringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivitystringlist1l('text/plain')java.lang.Stringtrueseperator0'text/plain'java.lang.Stringtrueconcatenated0'text/plain'0workfloworg.embl.ebi.escience.scuflworkers.java.StringListMergenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemax_datevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity2011/02/18net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeparametersXML_eSearchRetMax0db0maxdate0mindate0term0output00net.sf.taverna.t2.activitieswsdl-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivitydb0'text/plain'java.lang.Stringtrueterm0'text/plain'java.lang.StringtrueWebEnv0'text/plain'java.lang.StringtrueQueryKey0'text/plain'java.lang.Stringtrueusehistory0'text/plain'java.lang.Stringtruetool0'text/plain'java.lang.Stringtrueemail0'text/plain'java.lang.Stringtruefield0'text/plain'java.lang.Stringtruereldate0'text/plain'java.lang.Stringtruemindate0'text/plain'java.lang.Stringtruemaxdate0'text/plain'java.lang.Stringtruedatetype0'text/plain'java.lang.StringtrueRetStart0'text/plain'java.lang.StringtrueRetMax0'text/plain'java.lang.Stringtruerettype0'text/plain'java.lang.Stringtruesort0'text/plain'java.lang.Stringtrueoutput0'text/xml'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="eSearchRequest" name="parameters" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/esearch}eSearchRequest"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="db" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="term" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="WebEnv" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="QueryKey" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="usehistory" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="tool" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="email" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="field" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="reldate" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="mindate" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="maxdate" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="datetype" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="RetStart" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="RetMax" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="rettype" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="sort" qname="{http://www.w3.org/2001/XMLSchema}string" 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qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/esearch}>eSearchRequest>usehistory" /><s:basetype optional="true" unbounded="false" typename="string" name="tool" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/esearch}>eSearchRequest>tool" /><s:basetype optional="true" unbounded="false" typename="string" name="email" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/esearch}>eSearchRequest>email" /><s:basetype optional="true" unbounded="false" typename="string" name="field" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/esearch}>eSearchRequest>field" /><s:basetype optional="true" unbounded="false" typename="string" name="reldate" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/esearch}>eSearchRequest>reldate" /><s:basetype optional="true" unbounded="false" typename="string" name="mindate" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/esearch}>eSearchRequest>mindate" /><s:basetype optional="true" unbounded="false" typename="string" name="maxdate" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/esearch}>eSearchRequest>maxdate" /><s:basetype optional="true" unbounded="false" typename="string" name="datetype" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/esearch}>eSearchRequest>datetype" /><s:basetype optional="true" unbounded="false" typename="string" name="RetStart" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/esearch}>eSearchRequest>RetStart" /><s:basetype optional="true" unbounded="false" typename="string" name="RetMax" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/esearch}>eSearchRequest>RetMax" /><s:basetype optional="true" unbounded="false" typename="string" name="rettype" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/esearch}>eSearchRequest>rettype" /><s:basetype optional="true" unbounded="false" typename="string" name="sort" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/esearch}>eSearchRequest>sort" /></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGENE_RankPhenotypeTermspubmed_abstract_number0phenotype_term_counts0query_abstracts0phenotype_abstracts0phenotype_terms0cosine_vector_scores00concept_rankings00net.sf.taverna.t2.activitiesdataflow-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemax_return_genevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity500net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokePATHWAY_RankPhenotypeTermsquery_abstracts0phenotype_abstracts0pubmed_abstract_number0phenotype_term_counts0phenotype_terms0cosine_vector_scores00concept_rankings00net.sf.taverna.t2.activitiesdataflow-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesplit_search_terms_2string0regex0split11net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivitystring0'text/plain'java.lang.Stringtrueregex0'text/plain'java.lang.Stringtruesplit1l('text/plain')1workfloworg.embl.ebi.escience.scuflworkers.java.SplitByRegexnet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokepathway_and_abstractabstracts0pathway0output00net.sf.taverna.t2.activitiesbeanshell-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivitypathway0'text/plain'java.lang.Stringtrueabstracts0'text/plain'java.lang.Stringtrueoutput0'text/plain'0workflownet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeremove_nulls_3input0output00net.sf.taverna.t2.activitiesbeanshell-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivityinput0'text/plain'java.lang.Stringtrueoutput0'text/plain'0workflownet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemerge_outputs_2_2stringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivitystringlist1l('text/plain')java.lang.Stringtrueseperator0'text/plain'java.lang.Stringtrueconcatenated0'text/plain'0workfloworg.embl.ebi.escience.scuflworkers.java.StringListMergenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregex_2value00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity\nnet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeextract_termsinput0output00net.sf.taverna.t2.activitiesbeanshell-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivityinput0'text/plain'java.lang.Stringtrueoutput00workflownet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeadd_MeSH_to_stringinput0output00net.sf.taverna.t2.activitiesbeanshell-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivityinput0'text/plain'java.lang.Stringtrueoutput0'text/plain'0workflownet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSearch_PubMed_2Pathway_search_term0concat_data00net.sf.taverna.t2.activitiesdataflow-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeclean_text_2input0cleaned_text00net.sf.taverna.t2.activitiesdataflow-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050005net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegenerateTerminologyparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://projects.biotec.tu-dresden.de/DOG4DAG_TAVERNA/services/GoPubMedTermGeneration?wsdlgenerateTerminologynet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegenerateTerminology_inputtexts1applicationCode0output00net.sf.taverna.t2.activitieswsdl-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivityapplicationCode0'text/plain'falsetexts1l('text/plain')falsemaxNumberOfTerms0'text/plain'falseoutput0'text/xml'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="generateTerminology" name="parameters" qname="{http://server.gopubmedTermGenerationService.biotec.tud.de}generateTerminology"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="applicationCode" qname="{http://server.gopubmedTermGenerationService.biotec.tud.de}>generateTerminology>applicationCode" /><s:arraytype optional="true" unbounded="true" wrapped="false" typename="string" name="texts" qname="{http://server.gopubmedTermGenerationService.biotec.tud.de}>generateTerminology>texts"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype><s:basetype optional="true" unbounded="false" typename="int" name="maxNumberOfTerms" qname="{http://server.gopubmedTermGenerationService.biotec.tud.de}>generateTerminology>maxNumberOfTerms" /></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeapplicationCode_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity20110209_tavernanet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeremove_nullsinputgene_and_abstractabstractsgene_and_abstractpathwaysplit_search_termsregexsplit_search_termsstringmerge_outputs_2stringlistSearch_PubMedsearch_termSearch_PubMedmin_dateSearch_PubMedmax_dateSearch_PubMedmax_returnclean_textinputRemove_duplicate_genesstringlistsplit_gene_namesstringsplit_gene_namesregexremove_Nulls_2inputMerge_string_list_to_stringstringlistrun_eSearchparametersextractPMIDxpathextractPMIDxml-textremove_Nulls_4inputconcat_abstract_idsidconcat_abstract_idsabstract_textconcat_abstract_idsdate_textmerge_phenotype_abstractsabstractsmerge_phenotype_abstractsphenotypemerge_abstractsstringlistparametersXML_eSearchRetMaxparametersXML_eSearchdbparametersXML_eSearchmaxdateparametersXML_eSearchmindateparametersXML_eSearchtermmerge_abstract_idsstringlistmerge_datesstringlistFetch_Abstractspubmed_idsclean_text_3inputEncode_byte_to_base64bytesmerge_strings_2stringlistextract_abstractsinputmerge_search_and_termstermsmerge_search_and_termssearch_termextract_Terms_2xpathextract_Terms_2xml-textmerge_stringsstringlistremove_Nulls_5inputRemove_duplicate_strings_2stringlistsplit_by_regexregexsplit_by_regexstringclean_text_4file_direct_dataextract_terms_3inputmerge_term_counttermmerge_term_countcountsplit_extracted_termsstringsplit_extracted_termsregexmerge_pubmed_countstringlistmerge_extractedstringlistmerge_liststringlistextractCount_2xpathextractCount_2xml-textextractCountxpathextractCountxml-textparametersXML_1dbrun_eInforequestrun_eSearch_2requestrun_eSearch_requestdbrun_eSearch_requestrettyperun_eSearch_requesttermrun_eSearch_requestmindaterun_eSearch_requestmaxdateGENE_RankPhenotypeTermspubmed_abstract_numberGENE_RankPhenotypeTermsphenotype_term_countsGENE_RankPhenotypeTermsquery_abstractsGENE_RankPhenotypeTermsphenotype_abstractsGENE_RankPhenotypeTermsphenotype_termsPATHWAY_RankPhenotypeTermsquery_abstractsPATHWAY_RankPhenotypeTermsphenotype_abstractsPATHWAY_RankPhenotypeTermspubmed_abstract_numberPATHWAY_RankPhenotypeTermsphenotype_term_countsPATHWAY_RankPhenotypeTermsphenotype_termssplit_search_terms_2stringsplit_search_terms_2regexpathway_and_abstractabstractspathway_and_abstractpathwayremove_nulls_3inputmerge_outputs_2_2stringlistextract_termsinputadd_MeSH_to_stringinputSearch_PubMed_2Pathway_search_termclean_text_2inputgenerateTerminologyparametersgenerateTerminology_inputtextsgenerateTerminology_inputapplicationCodegene_abstractsphenotype_abstractsphenotype_termsphenotype_term_countspubmed_abstract_numbergene_cosinegene_term_enrichment_scorespathway_abstractspathway_cosine_vector_scorespathway_concept_rankings40bfde1b-6930-41fc-b616-a5f578a535c02011-02-11 12:15:18.756 GMT0c061808-75fd-4dfd-9ff7-ed77015684fd2011-02-10 16:45:07.766 GMT2964ebe6-e008-408e-ab98-08eb239fc6d02011-02-08 13:05:26.360 GMT411c7f97-71ea-4efc-9832-3d244cea610b2011-01-11 11:53:58.134 GMTc6b7062b-3107-4a49-9dca-8e2ab6b87fd72010-12-24 16:32:58.894 GMT8464fab9-2358-4b3b-b0a6-67305b9ea80b2011-02-09 11:26:19.571 GMT15af69a6-9f6e-4da4-8e54-7c5d6c4b7e2c2011-02-03 18:21:58.815 GMT55284e0e-0b2f-4c84-869e-dc50e34e99da2011-02-11 12:02:42.553 GMTThis workflow takes in a list of gene names and KEGG pathway descriptions, and searches the PubMed database for corresponding articles. Any matches to the genes are then retrieved (abstracts only). These abstracts are then used to calculate a cosine vector space between two sets of corpora (gene and phenotype, or pathway and phenotype).
The workflow counts the number of articles in the pubmed database in which each term occurs, and identifies the total number of articles in the entire PubMed database. It also identified the total number of articles within pubmed so that a term enrichment score may be calculated.
The workflow also takes in a document containing abstracts that are related to a particular phenotype. Scientiifc terms are then extracted from this text and given a weighting according to the number of terms that appear in the document. The higher the value the better the score.
This is given as: X = log((a / b) / (c / d))
where: a = number of occurnaces of individual terms in phenotype corpus
b = number of abstracts in entire phenotype corpus
c = number of occurnaces of individual terms in entire pubmed
d = number of articles in entire pubmed
Once this has been created, the pathways obtained from the QTL and microarray pathway analysis workflows are analysed. The documents from a search of each pathway in pubmed are merged into a single document of pathway abstracts. The (unweighted) phenotype terms are then searched in the pathways corpus. This will determine if the phenotype term is listed with the given pathway. The higher the value the better the score.
Each term is then assigned a weight as: Y = log((e / f) / (c /d))
where: a = number of occurnaces of individual terms in pathway corpus
b = number of abstracts in pathway corpus (per pathway)
c = number of occurnaces of individual terms in entire pubmed
d = number of articles in entire pubmed
The weighted terms are then given a link score. This is the total of: X + Y. This gives the link between the pathway and the phenotype a score / significance value. The higher the score the more "appropriate/interesting" the link between the pathway and the phenotype.
The terms are also ranked according to the number of pathways which have been given a weight. This is calculated as: W = ( X + Y). The higher the value the better the score.2011-02-18 13:41:03.756 GMTPaul Fisher2010-12-24 16:25:11.10 GMTThis workflow takes in a list of gene names and searches the PubMed database for corresponding articles. Any matches to the genes are then retrieved (abstracts only). These abstracts are then returned to the user.2010-12-24 16:25:11.10 GMTb04db057-6730-42b1-9e3f-68ae29870d782011-02-18 13:41:04.832 GMTPathway and Gene to Pubmed2011-02-10 16:05:04.3 GMTGene to Pubmed2010-12-24 16:25:11.10 GMTa1f6f265-068a-46ee-8966-36e3abb4ebe42011-02-02 15:23:46.908 GMT02b8d6bf-666d-4e32-ac76-ba0061020f152011-02-03 12:54:56.337 GMT21542038-b8c9-41da-bbc8-62d7afdcff092010-12-24 16:35:46.602 GMTcfd5b48e-ecdb-492f-a4c7-d154100153132010-12-27 17:24:27.435 GMTef82e651-933b-4c7e-81b8-2d4c3404ec632011-01-11 16:37:06.276 GMTcca35e36-81ae-464c-b04b-335af69bf3b32011-02-08 12:57:23.600 GMT9e7b600b-0c14-4a9f-bc37-166a1ee828852011-02-10 16:42:55.326 GMT5efb1e8b-e09e-4de8-8cab-a7352a0c2bb62011-02-03 13:17:30.347 GMT6d53d210-0330-427a-a460-3e356768af062011-02-18 12:37:31.989 GMT092666c7-cffc-4b88-b53a-0aaaa37037fa2011-02-08 12:37:26.587 GMT02b50687-d057-4b5e-99fd-a1ed4fdef4a92010-12-24 16:34:14.73 GMT37b26ab0-b32f-4cc5-99a1-0397999e86032011-02-04 13:07:47.695 GMTd5e42d7e-cfc2-4b8e-a7be-94d5308b379f2011-02-02 15:37:20.162 GMTc660e6ba-63d5-4b3b-a8c5-f5366b1983322011-02-08 13:10:22.904 GMTfc99edd7-1aa6-4bfd-90e4-66a0deb118812011-02-10 16:04:27.761 GMT901fac42-0863-4ed6-98d0-c9b02e4a44cb2011-02-10 16:43:26.718 GMT0a985d84-40d7-4c89-b498-cf74814f54e22011-02-11 12:17:06.28 GMTc305d0dc-235d-4124-ae7e-8e9cb556ca3a2011-02-10 16:05:18.843 GMT5d3fb7c1-6ab5-4e36-8cd2-0256f91eaa3d2011-02-15 17:27:40.353 GMTThis workflow takes in a list of gene names and KEGG pathway descriptions, and searches the PubMed database for corresponding articles. Any matches to the genes are then retrieved (abstracts only). These abstracts are then used to calculate a cosine vector space between two sets of corpora (gene and phenotype, or pathway and phenotype). 2011-02-18 13:39:31.496 GMT82efd57d-9b72-47d7-8ff0-85d303cc8c5c2011-02-18 12:45:38.357 GMT044c19bb-f91a-472d-8c76-f771380993772011-02-08 16:04:15.243 GMT472ec8c8-9b6c-4921-ad61-cbfcba71aa572011-02-04 14:05:40.76 GMTf0f4c256-5467-415a-bdf3-2394c18d6a762011-02-14 11:35:03.300 GMT630d0538-a24f-4b45-9132-dbd7931aad9f2011-02-02 15:20:31.627 GMTRankPhenotypeTermsphenotype_terms002010-12-25 19:50:04.935 GMTphenotype_abstracts002010-12-25 19:50:04.935 GMTtext/plain2010-12-25 19:50:04.935 GMTquery_abstracts00text/plain2010-12-25 19:50:04.935 GMT2010-12-25 19:50:04.935 GMTphenotype_term_counts00pubmed_abstract_number00concept_rankingstext/plain2010-12-25 19:50:04.951 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19:51:05.480 GMTThis workflow counts the number of articles in the pubmed database in which each term occurs, and identifies the total number of articles in the entire PubMed database. It also identified the total number of articles within pubmed so that a term enrichment score may be calculated.
The workflow also takes in a document containing abstracts that are related to a particular phenotype. Scientiifc terms are then extracted from this text and given a weighting according to the number of terms that appear in the document. The higher the value the better the score.
This is given as: X = log((a / b) / (c / d))
where: a = number of occurnaces of individual terms in phenotype corpus
b = number of abstracts in entire phenotype corpus
c = number of occurnaces of individual terms in entire pubmed
d = number of articles in entire pubmed
Once this has been created, the pathways obtained from the QTL and microarray pathway analysis workflows are analysed. The documents from a search of each pathway in pubmed are merged into a single document of pathway abstracts. The (unweighted) phenotype terms are then searched in the pathways corpus. This will determine if the phenotype term is listed with the given pathway. The higher the value the better the score.
Each term is then assigned a weight as: Y = log((e / f) / (c /d))
where: a = number of occurnaces of individual terms in pathway corpus
b = number of abstracts in pathway corpus (per pathway)
c = number of occurnaces of individual terms in entire pubmed
d = number of articles in entire pubmed
The weighted terms are then given a link score. This is the total of: X + Y. This gives the link between the pathway and the phenotype a score / significance value. The higher the score the more "appropriate/interesting" the link between the pathway and the phenotype.
The terms are also ranked according to the number of pathways which have been given a weight. This is calculated as: W = Sum( X + Y). The higher the value the better the score.2010-12-25 19:50:14.124 GMTThis workflow calculates the cosine vector space between two sets of corpora. The workflow then removes any null values from the output. this is some extra text vbeing added
It also counts the number of articles in the pubmed database in which each term occurs, and identifies the total number of articles in the entire PubMed database. It also identified the total number of articles within pubmed so that a term enrichment score may be calculated.
The workflow also takes in a document containing abstracts that are related to a particular phenotype. Scientiifc terms are then extracted from this text and given a weighting according to the number of terms that appear in the document. The higher the value the better the score.
This is given as: X = log((a / b) / (c / d))
where: a = number of occurnaces of individual terms in phenotype corpus
b = number of abstracts in entire phenotype corpus
c = number of occurnaces of individual terms in entire pubmed
d = number of articles in entire pubmed
Once this has been created, the pathways obtained from the QTL and microarray pathway analysis workflows are analysed. The documents from a search of each pathway in pubmed are merged into a single document of pathway abstracts. The (unweighted) phenotype terms are then searched in the pathways corpus. This will determine if the phenotype term is listed with the given pathway. The higher the value the better the score.
Each term is then assigned a weight as: Y = log((e / f) / (c /d))
where: a = number of occurnaces of individual terms in pathway corpus
b = number of abstracts in pathway corpus (per pathway)
c = number of occurnaces of individual terms in entire pubmed
d = number of articles in entire pubmed
The weighted terms are then given a link score. This is the total of: X + Y. This gives the link between the pathway and the phenotype a score / significance value. The higher the score the more "appropriate/interesting" the link between the pathway and the phenotype.
The terms are also ranked according to the number of pathways which have been given a weight. This is calculated as: W = Sum( X + Y). The higher the value the better the score.2011-02-01 11:17:50.743 GMT97d23587-e50d-4926-b62e-2becaded5c602010-12-27 14:55:31.822 GMT87e7ef54-f110-4027-9765-9d0a837efb2a2011-02-02 15:05:20.786 GMT16ad416d-9049-42ce-a263-8d28ed90e6d42010-12-27 14:49:02.865 GMTPaul Fisher2010-12-25 19:50:14.124 GMT38f5f9ed-2361-431b-bcc4-e74131eec66a2011-01-31 13:08:42.909 GMT9ddd20a9-4d5b-4fec-bd5b-a045741f11de2011-02-02 15:14:54.159 GMTRank Phenotype Terms2010-12-25 19:50:14.124 GMT9f53e57c-a222-49e1-ae05-bae6e891dac92010-12-25 19:55:34.403 GMT79bcd1ec-38a6-4634-8eea-21a1edc3e34b2010-12-25 19:59:38.23 GMT7ce75b2a-baa5-4231-8ded-7a763e6cd69c2011-02-04 13:07:45.14 GMT0f3ee5e9-60b7-43c4-b940-4bc2482c85e02010-12-27 15:03:30.135 GMTbed0ff14-4766-41bb-a15d-f1d6bf98cc4d2010-12-27 15:05:03.812 GMTac1f2dc2-f9a9-4c74-86ff-377b00f157102011-02-01 11:17:52.110 GMTe27c607d-a2ff-405a-9fb1-c33f4c543d7e2010-12-26 12:29:03.697 GMTcc5d8438-319a-4327-9261-c2752656150c2011-01-31 13:10:30.83 GMTclean_textinput002010-12-27 17:24:06.126 GMTtext/plain2010-12-27 17:24:06.126 GMTcleaned_textclean_textfile_direct_data0report00output00net.sf.taverna.t2.activitiessoaplab-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.soaplab.SoaplabActivityhttp://phoebus.cs.man.ac.uk:1977/axis/services/text_mining.clean_text01.00net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokestringToBytesstring0bytes00net.sf.taverna.t2.activitiesbeanshell-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivitystring0'text/plain'java.lang.Stringtruebytes0'application/octet-stream'0workflownet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeEncode_byte___to_base64bytes0base6400net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivitybytes0'application/octet-stream'[Btruebase640'text/plain'0workflowcommons-codeccommons-codec1.31635363350commons-codec:commons-codec:1.3org.embl.ebi.escience.scuflworkers.java.EncodeBase64net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeclean_textfile_direct_datastringToBytesstringEncode_byte___to_base64bytescleaned_text1d592ca5-aba5-4bf5-b657-bd90702f91862010-12-27 17:24:06.578 GMT2010-12-27 17:24:06.438 GMTclean_text2010-12-27 17:24:06.438 GMT2010-12-27 17:24:06.438 GMTPathwaytoPubMedPathway_search_term00text/plain2010-12-24 16:55:18.959 GMT2010-12-24 16:55:18.959 GMTconcat_datatext/plain2010-12-24 16:55:18.959 GMTxpathvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity/*[local-name(.)='eSearchResult']/*[local-name(.)='IdList']/*[local-name(.)='Id']net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokepubmed_databasevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivitypubmednet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeextractPMIDxml-text0xpath0nodelist11nodelistAsXML11net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivityxpath0'text/plain'java.lang.Stringtruexml-text0'text/xml'java.lang.Stringtruenodelist1l('text/plain')1nodelistAsXML1l('text/plain')1workflowdom4jdom4j1.6716010169dom4j:dom4j:1.6net.sourceforge.taverna.scuflworkers.xml.XPathTextWorkernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemerge_abstract_idsstringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivitystringlist1l('text/plain')java.lang.Stringtrueseperator0'text/plain'java.lang.Stringtrueconcatenated0'text/plain'0workfloworg.embl.ebi.escience.scuflworkers.java.StringListMergenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeconcat_abstract_idsid0abstract_text0date_text0output00net.sf.taverna.t2.activitiesbeanshell-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivityid0'text/plain'java.lang.Stringtrueabstract_text0'text/plain'java.lang.Stringtruedate_text0'text/plain'java.lang.Stringtrueoutput00workflownet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemax_returnvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity500net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemerge_abstractsstringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivitystringlist1l('text/plain')java.lang.Stringtrueseperator0'text/plain'java.lang.Stringtrueconcatenated0'text/plain'0workfloworg.embl.ebi.escience.scuflworkers.java.StringListMergenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeparametersXML_eFecthRetMax0db0term0maxdate0mindate0output00net.sf.taverna.t2.activitieswsdl-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivitydb0'text/plain'java.lang.Stringtrueterm0'text/plain'java.lang.StringtrueWebEnv0'text/plain'java.lang.StringtrueQueryKey0'text/plain'java.lang.Stringtrueusehistory0'text/plain'java.lang.Stringtruetool0'text/plain'java.lang.Stringtrueemail0'text/plain'java.lang.Stringtruefield0'text/plain'java.lang.Stringtruereldate0'text/plain'java.lang.Stringtruemindate0'text/plain'java.lang.Stringtruemaxdate0'text/plain'java.lang.Stringtruedatetype0'text/plain'java.lang.StringtrueRetStart0'text/plain'java.lang.StringtrueRetMax0'text/plain'java.lang.Stringtruerettype0'text/plain'java.lang.Stringtruesort0'text/plain'java.lang.Stringtrueoutput0'text/xml'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="eSearchRequest" name="parameters" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/esearch}eSearchRequest"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="db" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="term" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="WebEnv" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="QueryKey" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="usehistory" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="tool" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="email" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="field" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="reldate" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="mindate" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="maxdate" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="datetype" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="RetStart" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="RetMax" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="rettype" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="sort" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemerge_datesstringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivitystringlist1l('text/plain')java.lang.Stringtrueseperator0'text/plain'java.lang.Stringtrueconcatenated0'text/plain'0workfloworg.embl.ebi.escience.scuflworkers.java.StringListMergenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokerun_eSearchparameters0parameters00attachmentList11net.sf.taverna.t2.activitieswsdl-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdlrun_eSearchnet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize5net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRetrive_abstractspubmed_ids0date11abstract11net.sf.taverna.t2.activitiesdataflow-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize5net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050005net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemaxdate_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity2010/10/31net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemindate_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity2000/01/01net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeextractPMIDxml-textextractPMIDxpathmerge_abstract_idsstringlistconcat_abstract_idsidconcat_abstract_idsabstract_textconcat_abstract_idsdate_textmerge_abstractsstringlistparametersXML_eFecthRetMaxparametersXML_eFecthdbparametersXML_eFecthtermparametersXML_eFecthmaxdateparametersXML_eFecthmindatemerge_datesstringlistrun_eSearchparametersRetrive_abstractspubmed_idsconcat_data36081486-0b5f-4de1-b707-150a6e0898dc2010-12-24 16:55:35.572 GMT4f3a65a1-f91a-4c53-9fac-4561b2747d4d2010-12-24 16:57:22.562 GMTThis workflow takes in a list of KEGG pathway descriptions and a stop_list of KEGG pathway descriptions. These patwhays are then compared, and those in the stop list are removed. The workflow then extracts the pathway process from the KEGG formatted pathway descriptions output. It takes in a list of KEGG pathway descriptions and returns a list of pathways, without the KEGG pathway identifier or the species from which it came (e.g. - mus musculus (mouse) ). These are passed to the eSearch function and searched for in PubMed. Those abstracts found are returned to the user2010-12-24 16:55:20.448 GMTPathway to PubMed2010-12-24 16:55:20.449 GMTPaul Fisher2010-12-24 16:55:20.448 GMT3ce552d8-caa2-44cd-ab8a-2cd6fa967f942011-02-11 12:16:15.795 GMTf843ae51-1d3d-4697-aa59-5977fc2b36792010-12-24 17:34:22.711 GMTPathwaytoPubMedsearch_term002010-12-24 16:25:09.726 GMTtext/plain2010-12-24 16:25:09.726 GMTmin_date00max_date00max_return00concat_datatext/plain2010-12-24 16:25:09.726 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/></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRetrive_abstractspubmed_ids0date11abstract11net.sf.taverna.t2.activitiesdataflow-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize5net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050005net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeconcat_abstract_idsdate_textconcat_abstract_idsabstract_textconcat_abstract_idsidrun_eSearchparametersmerge_datesstringlistmerge_abstract_idsstringlistmerge_abstractsstringlistextractPMIDxml-textextractPMIDxpathparametersXML_eFecthtermparametersXML_eFecthdbparametersXML_eFecthRetMaxparametersXML_eFecthmaxdateparametersXML_eFecthmindateRetrive_abstractspubmed_idsconcat_dataPaul Fisher2010-12-24 16:25:11.9 GMTThis workflow takes in a list of KEGG pathway descriptions and a stop_list of KEGG pathway descriptions. These patwhays are then compared, and those in the stop list are removed. The workflow then extracts the pathway process from the KEGG formatted pathway descriptions output. It takes in a list of KEGG pathway descriptions and returns a list of pathways, without the KEGG pathway identifier or the species from which it came (e.g. - mus musculus (mouse) ). These are passed to the eSearch function and searched for in PubMed. Those abstracts found are returned to the user2010-12-24 16:25:11.9 GMTa1afe21b-b3e9-4f41-8de4-5910263a75df2010-12-24 16:26:19.779 GMT968d2b6b-54ce-499a-9748-2e1f8d3b64b22010-12-24 16:35:34.138 GMT685e516d-282a-4921-96f0-5bdf6dad3c7c2010-12-24 16:34:03.113 GMT5997c366-c02d-4830-8fba-93aa0bf0027c2011-02-11 12:14:55.115 GMTb284797f-907b-494b-be67-0a922a30a74d2011-02-02 15:23:00.575 GMTPathway to PubMed2010-12-24 16:25:11.9 GMTclean_textinput002010-12-27 17:25:46.93 GMTtext/plain2010-12-27 17:25:46.93 GMTcleaned_textclean_textfile_direct_data0output00report00net.sf.taverna.t2.activitiessoaplab-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.soaplab.SoaplabActivityhttp://phoebus.cs.man.ac.uk:1977/axis/services/text_mining.clean_text01.00net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokestringToBytesstring0bytes00net.sf.taverna.t2.activitiesbeanshell-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivitystring0'text/plain'java.lang.Stringtruebytes0'application/octet-stream'0workflownet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeEncode_byte___to_base64bytes0base6400net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivitybytes0'application/octet-stream'[Btruebase640'text/plain'0workflowcommons-codeccommons-codec1.31635363350commons-codec:commons-codec:1.3org.embl.ebi.escience.scuflworkers.java.EncodeBase64net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeclean_textfile_direct_datastringToBytesstringEncode_byte___to_base64bytescleaned_textclean_text2010-12-27 17:25:46.405 GMTd7c165ea-ac2c-4b92-be21-b219a0c1376a2010-12-27 17:25:46.576 GMT2010-12-27 17:25:46.405 GMT2010-12-27 17:25:46.405 GMTXPathPubmedIdspubmed_ids00text/plain2010-12-24 17:14:54.310 GMT2010-12-24 17:14:54.310 GMTpubmed_datestext/plain2010-12-24 17:14:54.310 GMTabstractstext/plain2010-12-24 17:14:54.310 GMTxpath2value00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity/*[local-name(.)='eFetchResult']/*[local-name(.)='PubmedArticleSet']/*[local-name(.)='PubmedArticle']/*[local-name(.)='MedlineCitation']/*[local-name(.)='DateCreated']/*[local-name(.)='Year']net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeextractAbstractxpath0xml-text0nodelist11nodelistAsXML11net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivityxpath0'text/plain'java.lang.Stringtruexml-text0'text/xml'java.lang.Stringtruenodelist1l('text/plain')1nodelistAsXML1l('text/plain')1workflowdom4jdom4j1.6716010169dom4j:dom4j:1.6net.sourceforge.taverna.scuflworkers.xml.XPathTextWorkernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokexpathvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity/*[local-name(.)='eFetchResult']/*[local-name(.)='PubmedArticleSet']/*[local-name(.)='PubmedArticle']/*[local-name(.)='MedlineCitation']/*[local-name(.)='Article']/*[local-name(.)='Abstract']/*[local-name(.)='AbstractText']net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeparametersXMLid0db0output00net.sf.taverna.t2.activitieswsdl-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivitydb0'text/plain'java.lang.Stringtrueid0'text/plain'java.lang.StringtrueWebEnv0'text/plain'java.lang.Stringtruequery_key0'text/plain'java.lang.Stringtruetool0'text/plain'java.lang.Stringtrueemail0'text/plain'java.lang.Stringtrueretstart0'text/plain'java.lang.Stringtrueretmax0'text/plain'java.lang.Stringtruerettype0'text/plain'java.lang.Stringtruestrand0'text/plain'java.lang.Stringtrueseq_start0'text/plain'java.lang.Stringtrueseq_stop0'text/plain'java.lang.Stringtruecomplexity0'text/plain'java.lang.Stringtruereport0'text/plain'java.lang.Stringtrueoutput0'text/xml'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="eFetchRequest" name="parameters" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}eFetchRequest"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="db" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>db" /><s:basetype optional="true" unbounded="false" typename="string" name="id" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>id" /><s:basetype optional="true" unbounded="false" typename="string" name="WebEnv" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>WebEnv" /><s:basetype optional="true" unbounded="false" typename="string" name="query_key" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>query_key" /><s:basetype optional="true" unbounded="false" typename="string" name="tool" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>tool" /><s:basetype optional="true" unbounded="false" typename="string" name="email" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>email" /><s:basetype optional="true" unbounded="false" typename="string" name="retstart" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>retstart" /><s:basetype optional="true" unbounded="false" typename="string" name="retmax" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>retmax" /><s:basetype optional="true" unbounded="false" typename="string" name="rettype" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>rettype" /><s:basetype optional="true" unbounded="false" typename="string" name="strand" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>strand" /><s:basetype optional="true" unbounded="false" typename="string" name="seq_start" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>seq_start" /><s:basetype optional="true" unbounded="false" typename="string" name="seq_stop" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>seq_stop" /><s:basetype optional="true" unbounded="false" typename="string" name="complexity" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>complexity" /><s:basetype optional="true" unbounded="false" typename="string" name="report" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>report" /></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokedatabasevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivitypubmednet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeextractDatesxpath0xml-text0nodelist11nodelistAsXML11net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivityxpath0'text/plain'java.lang.Stringtruexml-text0'text/xml'java.lang.Stringtruenodelist1l('text/plain')1nodelistAsXML1l('text/plain')1workflowdom4jdom4j1.6716010169dom4j:dom4j:1.6net.sourceforge.taverna.scuflworkers.xml.XPathTextWorkernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokerun_eFetchinpp0outp00net.sf.taverna.t2.activitieswsdl-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://eutils.ncbi.nlm.nih.gov/soap/v2.0/efetch_pubmed.wsdlrun_eFetchnet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize5net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050005net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeextractAbstractxpathextractAbstractxml-textparametersXMLidparametersXMLdbextractDatesxpathextractDatesxml-textrun_eFetchinpppubmed_datesabstractsThis workflow takes in a number of search terms (as used in the normal PubMed interface) and retrieves a list of PubMed ids in a list format.2010-12-24 17:14:54.640 GMTfa9e3c15-b654-4364-b0ce-dd4f1bab3f6f2010-12-24 17:36:31.757 GMTXPath Pubmed Ids2010-12-24 17:14:54.640 GMT0d5a76a5-82c8-4719-9b78-afa89256efca2010-12-24 17:17:15.417 GMTPaul Fisher2010-12-24 17:14:54.640 GMTXPathPubmedIdspubmed_ids00text/plain2010-12-24 16:55:19.979 GMT2010-12-24 16:55:19.979 GMTabstracttext/plain2010-12-24 16:55:19.979 GMTdatetext/plain2010-12-24 16:55:19.979 GMTdatabasevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivitypubmednet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokexpath_2value00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity/*[local-name(.)='eFetchResult']/*[local-name(.)='PubmedArticleSet']/*[local-name(.)='PubmedArticle']/*[local-name(.)='MedlineCitation']/*[local-name(.)='DateCreated']/*[local-name(.)='Year']net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeextractAbstractxpath0xml-text0nodelist11nodelistAsXML11net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivityxpath0'text/plain'java.lang.Stringtruexml-text0'text/xml'java.lang.Stringtruenodelist1l('text/plain')1nodelistAsXML1l('text/plain')1workflowdom4jdom4j1.6716010169dom4j:dom4j:1.6net.sourceforge.taverna.scuflworkers.xml.XPathTextWorkernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokexpathvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity/*[local-name(.)='eFetchResult']/*[local-name(.)='PubmedArticleSet']/*[local-name(.)='PubmedArticle']/*[local-name(.)='MedlineCitation']/*[local-name(.)='Article']/*[local-name(.)='Abstract']/*[local-name(.)='AbstractText']net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeextractDatesxpath0xml-text0nodelistAsXML11nodelist11net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivityxpath0'text/plain'java.lang.Stringtruexml-text0'text/xml'java.lang.Stringtruenodelist1l('text/plain')1nodelistAsXML1l('text/plain')1workflowdom4jdom4j1.6716010169dom4j:dom4j:1.6net.sourceforge.taverna.scuflworkers.xml.XPathTextWorkernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeparametersXMLid0db0output00net.sf.taverna.t2.activitieswsdl-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivitydb0'text/plain'java.lang.Stringtrueid0'text/plain'java.lang.StringtrueWebEnv0'text/plain'java.lang.Stringtruequery_key0'text/plain'java.lang.Stringtruetool0'text/plain'java.lang.Stringtrueemail0'text/plain'java.lang.Stringtrueretstart0'text/plain'java.lang.Stringtrueretmax0'text/plain'java.lang.Stringtruerettype0'text/plain'java.lang.Stringtruestrand0'text/plain'java.lang.Stringtrueseq_start0'text/plain'java.lang.Stringtrueseq_stop0'text/plain'java.lang.Stringtruecomplexity0'text/plain'java.lang.Stringtruereport0'text/plain'java.lang.Stringtrueoutput0'text/xml'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="eFetchRequest" name="parameters" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}eFetchRequest"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="db" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>db" /><s:basetype optional="true" unbounded="false" typename="string" name="id" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>id" /><s:basetype optional="true" unbounded="false" typename="string" name="WebEnv" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>WebEnv" /><s:basetype optional="true" unbounded="false" typename="string" name="query_key" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>query_key" /><s:basetype optional="true" unbounded="false" typename="string" name="tool" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>tool" /><s:basetype optional="true" unbounded="false" typename="string" name="email" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>email" /><s:basetype optional="true" unbounded="false" typename="string" name="retstart" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>retstart" /><s:basetype optional="true" unbounded="false" typename="string" name="retmax" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>retmax" /><s:basetype optional="true" unbounded="false" typename="string" name="rettype" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>rettype" /><s:basetype optional="true" unbounded="false" typename="string" name="strand" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>strand" /><s:basetype optional="true" unbounded="false" typename="string" name="seq_start" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>seq_start" /><s:basetype optional="true" unbounded="false" typename="string" name="seq_stop" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>seq_stop" /><s:basetype optional="true" unbounded="false" typename="string" name="complexity" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>complexity" /><s:basetype optional="true" unbounded="false" typename="string" name="report" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>report" /></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokerun_eFetchinpp0outp00net.sf.taverna.t2.activitieswsdl-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://eutils.ncbi.nlm.nih.gov/soap/v2.0/efetch_pubmed.wsdlrun_eFetchnet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize5net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050005net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeextractAbstractxpathextractAbstractxml-textextractDatesxpathextractDatesxml-textparametersXMLidparametersXMLdbrun_eFetchinppabstractdate70eb97e7-d5f9-489a-a4f9-f4540b78b2452010-12-24 16:55:35.922 GMTXPath Pubmed Ids2010-12-24 16:55:20.448 GMTPaul Fisher2010-12-24 16:55:20.448 GMTThis workflow takes in a number of search terms (as used in the normal PubMed interface) and retrieves a list of PubMed ids in a list format.2010-12-24 16:55:20.448 GMTf4e5022f-2351-4c05-a8f5-9eb5702379f52010-12-24 17:34:13.229 GMT22481a7b-eb54-4b80-a29c-89cf6c462ae02010-12-24 17:32:41.1 GMTclean_textinput00text/plain2010-12-27 17:24:56.320 GMT2010-12-27 17:24:56.320 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17:24:56.804 GMT2010-12-27 17:24:56.632 GMT2010-12-27 17:24:56.632 GMTclean_text2010-12-27 17:24:56.632 GMTXPathPubmedIdspubmed_ids002010-12-24 16:25:10.417 GMTtext/plain2010-12-24 16:25:10.417 GMTabstracttext/plain2010-12-24 16:25:10.417 GMTdatetext/plain2010-12-24 16:25:10.418 GMTxpathvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity/*[local-name(.)='eFetchResult']/*[local-name(.)='PubmedArticleSet']/*[local-name(.)='PubmedArticle']/*[local-name(.)='MedlineCitation']/*[local-name(.)='Article']/*[local-name(.)='Abstract']/*[local-name(.)='AbstractText']net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokexpath_2value00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity/*[local-name(.)='eFetchResult']/*[local-name(.)='PubmedArticleSet']/*[local-name(.)='PubmedArticle']/*[local-name(.)='MedlineCitation']/*[local-name(.)='DateCreated']/*[local-name(.)='Year']net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokerun_eFetchinpp0attachmentList11outp00net.sf.taverna.t2.activitieswsdl-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://www.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/efetch_pubmed.wsdlrun_eFetchnet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050005net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeextractDatesxml-text0xpath0nodelist11nodelistAsXML11net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivityxpath0'text/plain'java.lang.Stringtruexml-text0'text/xml'java.lang.Stringtruenodelist1l('text/plain')1nodelistAsXML1l('text/plain')1workflowdom4jdom4j1.6716010169dom4j:dom4j:1.6net.sourceforge.taverna.scuflworkers.xml.XPathTextWorkernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeextractAbstractxml-text0xpath0nodelistAsXML11nodelist11net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivityxpath0'text/plain'java.lang.Stringtruexml-text0'text/xml'java.lang.Stringtruenodelist1l('text/plain')1nodelistAsXML1l('text/plain')1workflowdom4jdom4j1.6716010169dom4j:dom4j:1.6net.sourceforge.taverna.scuflworkers.xml.XPathTextWorkernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeinppXMLid0output00net.sf.taverna.t2.activitieswsdl-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivityid0'text/plain'java.lang.StringtrueWebEnv0'text/plain'java.lang.Stringtruequery_key0'text/plain'java.lang.Stringtruetool0'text/plain'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xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="eFetchRequest" name="inpp" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch_pubmed}eFetchRequest"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="id" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch_pubmed}>eFetchRequest>id" /><s:basetype optional="true" unbounded="false" typename="string" name="WebEnv" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch_pubmed}>eFetchRequest>WebEnv" /><s:basetype optional="true" unbounded="false" typename="string" name="query_key" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch_pubmed}>eFetchRequest>query_key" /><s:basetype optional="true" unbounded="false" typename="string" name="tool" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch_pubmed}>eFetchRequest>tool" /><s:basetype optional="true" unbounded="false" typename="string" name="email" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch_pubmed}>eFetchRequest>email" /><s:basetype optional="true" unbounded="false" typename="string" name="retstart" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch_pubmed}>eFetchRequest>retstart" /><s:basetype optional="true" unbounded="false" typename="string" name="retmax" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch_pubmed}>eFetchRequest>retmax" /><s:basetype optional="true" unbounded="false" typename="string" name="rettype" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch_pubmed}>eFetchRequest>rettype" /></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokerun_eFetchinppextractDatesxml-textextractDatesxpathextractAbstractxml-textextractAbstractxpathinppXMLidabstractdate5cea1753-adae-440d-b871-876d38b84ff62010-12-24 16:26:20.146 GMTPaul Fisher2010-12-24 16:25:11.6 GMT0e12e023-764d-4bf0-a829-2d7e97d876e02010-12-24 16:35:09.315 GMTThis workflow takes in a number of search terms (as used in the normal PubMed interface) and retrieves a list of PubMed ids in a list format.2010-12-24 16:25:11.6 GMTXPath Pubmed Ids2010-12-24 16:25:11.6 GMT