GenetoPubmedgene_names00 2010-12-24 16:25:08.998 GMT text/plain 2010-12-24 16:25:08.996 GMT Phenotype_search_term00gene_abstracts text/plain 2010-12-24 16:25:09.3 GMT phenotype_abstractsphenotype_termsphenotype_term_countspubmed_abstract_numbergene_cosinegene_term_enrichment_scoresregexvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity \n net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.BeanshellActivity input 0 'text/plain' java.lang.String true output 0 'text/plain' 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.BeanshellActivity pathway 0 'text/plain' java.lang.String true abstracts 0 'text/plain' java.lang.String true output 0 'text/plain' 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.LocalworkerActivity string 0 'text/plain' java.lang.String true regex 0 'text/plain' java.lang.String true split 1 l('text/plain') 1 workflow org.embl.ebi.escience.scuflworkers.java.SplitByRegex net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true seperator 0 'text/plain' java.lang.String true concatenated 0 'text/plain' 0 workflow org.embl.ebi.escience.scuflworkers.java.StringListMerge net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.Parallelize 5 net.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.Retry 1.0 1000 5000 5 net.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.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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 \n net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true strippedlist 1 l('text/plain') 1 workflow org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.LocalworkerActivity string 0 'text/plain' java.lang.String true regex 0 'text/plain' java.lang.String true split 1 l('text/plain') 1 workflow org.embl.ebi.escience.scuflworkers.java.SplitByRegex net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.BeanshellActivity input 0 'text/plain' java.lang.String true output 0 'text/plain' 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true seperator 0 'text/plain' java.lang.String true concatenated 0 'text/plain' 0 workflow org.embl.ebi.escience.scuflworkers.java.StringListMerge net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.WSDLActivity http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl run_eSearch net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.StringConstantActivity 2000/01/01 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.LocalworkerActivity xpath 0 'text/plain' java.lang.String true xml-text 0 'text/xml' java.lang.String true nodelist 1 l('text/plain') 1 nodelistAsXML 1 l('text/plain') 1 workflow dom4j dom4j 1.6 716010169 dom4j:dom4j:1.6 net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.BeanshellActivity input 0 'text/plain' java.lang.String true output 0 'text/plain' 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.BeanshellActivity id 0 'text/plain' java.lang.String true abstract_text 0 'text/plain' java.lang.String true date_text 0 'text/plain' java.lang.String true output 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.StringConstantActivity 5000 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.StringConstantActivity pubmed net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.BeanshellActivity phenotype 0 'text/plain' java.lang.String true abstracts 0 'text/plain' java.lang.String true output 0 'text/plain' 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true seperator 0 'text/plain' java.lang.String true concatenated 0 'text/plain' 0 workflow org.embl.ebi.escience.scuflworkers.java.StringListMerge net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.StringConstantActivity 2011/01/31 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.XMLInputSplitterActivity db 0 'text/plain' java.lang.String true term 0 'text/plain' java.lang.String true WebEnv 0 'text/plain' java.lang.String true QueryKey 0 'text/plain' java.lang.String true usehistory 0 'text/plain' java.lang.String true tool 0 'text/plain' java.lang.String true email 0 'text/plain' java.lang.String true field 0 'text/plain' java.lang.String true reldate 0 'text/plain' java.lang.String true mindate 0 'text/plain' java.lang.String true maxdate 0 'text/plain' java.lang.String true datetype 0 'text/plain' java.lang.String true RetStart 0 'text/plain' java.lang.String true RetMax 0 'text/plain' java.lang.String true rettype 0 'text/plain' java.lang.String true sort 0 'text/plain' java.lang.String true output 0 '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.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true seperator 0 'text/plain' java.lang.String true concatenated 0 'text/plain' 0 workflow org.embl.ebi.escience.scuflworkers.java.StringListMerge net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true seperator 0 'text/plain' java.lang.String true concatenated 0 'text/plain' 0 workflow org.embl.ebi.escience.scuflworkers.java.StringListMerge net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFetch_Abstractspubmed_ids0pubmed_dates11abstracts11net.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.Parallelize 5 net.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.Retry 1.0 1000 5000 5 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeclean_text_3input0cleaned_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.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.LocalworkerActivity bytes 0 'application/octet-stream' [B true base64 0 'text/plain' 0 workflow commons-codec commons-codec 1.3 1635363350 commons-codec:commons-codec:1.3 org.embl.ebi.escience.scuflworkers.java.EncodeBase64 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemerge_strings_2stringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true seperator 0 'text/plain' java.lang.String true concatenated 0 'text/plain' 0 workflow org.embl.ebi.escience.scuflworkers.java.StringListMerge net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregex_3value00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity \n net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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(.)='generateTerminologyResponse']/*[local-name(.)='return'] net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeextract_abstractsinput0output_search00output00net.sf.taverna.t2.activitiesbeanshell-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivity input 0 'text/plain' java.lang.String true output 0 'text/plain' 0 output_search 0 'text/plain' 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemerge_search_and_termsterms0search_term0output00net.sf.taverna.t2.activitiesbeanshell-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivity terms 0 'text/plain' java.lang.String true search_term 0 'text/plain' java.lang.String true output 0 'text/plain' 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeextract_Terms_2xpath0xml-text0nodelistAsXML11nodelist11net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivity xpath 0 'text/plain' java.lang.String true xml-text 0 'text/xml' java.lang.String true nodelist 1 l('text/plain') 1 nodelistAsXML 1 l('text/plain') 1 workflow dom4j dom4j 1.6 716010169 dom4j:dom4j:1.6 net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemerge_stringsstringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true seperator 0 'text/plain' java.lang.String true concatenated 0 'text/plain' 0 workflow org.embl.ebi.escience.scuflworkers.java.StringListMerge net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeremove_Nulls_5input0output00net.sf.taverna.t2.activitiesbeanshell-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivity input 0 'text/plain' java.lang.String true output 0 'text/plain' 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRemove_duplicate_strings_2stringlist1strippedlist11net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true strippedlist 1 l('text/plain') 1 workflow org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesplit_by_regexregex0string0split11net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivity string 0 'text/plain' java.lang.String true regex 0 'text/plain' java.lang.String true split 1 l('text/plain') 1 workflow org.embl.ebi.escience.scuflworkers.java.SplitByRegex net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeclean_text_4file_direct_data0output00report00net.sf.taverna.t2.activitiessoaplab-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.soaplab.SoaplabActivity http://phoebus.cs.man.ac.uk:1977/axis/services/text_mining.clean_text 0 1.0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokepubmed_database_2value00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity pubmed net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokexpath_3value00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity /*[local-name(.)='eSearchResult']/*[local-name(.)='Count'] net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokecountvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity count net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokexpath_countvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity /*[local-name(.)='eInfoResult']/*[local-name(.)='DbInfo']/*[local-name(.)='Count'] net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeeSearch_databasevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity pubmed net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregular_expression_2value00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity \n net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeextract_terms_3input0output00net.sf.taverna.t2.activitiesbeanshell-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivity input 0 'text/plain' java.lang.String true output 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemerge_term_countterm0count0output00net.sf.taverna.t2.activitiesbeanshell-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivity term 0 'text/plain' java.lang.String true count 0 'text/plain' java.lang.String true output 0 'text/plain' 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesplit_extracted_termsstring0regex0split11net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivity string 0 'text/plain' java.lang.String true regex 0 'text/plain' java.lang.String true split 1 l('text/plain') 1 workflow org.embl.ebi.escience.scuflworkers.java.SplitByRegex net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemerge_pubmed_countstringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true seperator 0 'text/plain' java.lang.String true concatenated 0 'text/plain' 0 workflow org.embl.ebi.escience.scuflworkers.java.StringListMerge net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemerge_extractedstringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true seperator 0 'text/plain' java.lang.String true concatenated 0 'text/plain' 0 workflow org.embl.ebi.escience.scuflworkers.java.StringListMerge net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemerge_liststringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true seperator 0 'text/plain' java.lang.String true concatenated 0 'text/plain' 0 workflow org.embl.ebi.escience.scuflworkers.java.StringListMerge net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeextractCount_2xpath0xml-text0nodelist11nodelistAsXML11net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivity xpath 0 'text/plain' java.lang.String true xml-text 0 'text/xml' java.lang.String true nodelist 1 l('text/plain') 1 nodelistAsXML 1 l('text/plain') 1 workflow dom4j dom4j 1.6 716010169 dom4j:dom4j:1.6 net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeextractCountxpath0xml-text0nodelistAsXML11nodelist11net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivity xpath 0 'text/plain' java.lang.String true xml-text 0 'text/xml' java.lang.String true nodelist 1 l('text/plain') 1 nodelistAsXML 1 l('text/plain') 1 workflow dom4j dom4j 1.6 716010169 dom4j:dom4j:1.6 net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeparametersXML_1db0output00net.sf.taverna.t2.activitieswsdl-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity db 0 'text/plain' java.lang.String true tool 0 'text/plain' java.lang.String true email 0 'text/plain' java.lang.String true output 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="eInfoRequest" name="parameters" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/einfo}eInfoRequest"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="db" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/einfo}&gt;eInfoRequest&gt;db" /><s:basetype optional="true" unbounded="false" typename="string" name="tool" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/einfo}&gt;eInfoRequest&gt;tool" /><s:basetype optional="true" unbounded="false" typename="string" name="email" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/einfo}&gt;eInfoRequest&gt;email" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokerun_eInforequest0result00net.sf.taverna.t2.activitieswsdl-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.wsdl.WSDLActivity http://eutils.ncbi.nlm.nih.gov/soap/v2.0/eutils.wsdl run_eInfo net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 5 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokerun_eSearch_2request0result00net.sf.taverna.t2.activitieswsdl-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.wsdl.WSDLActivity http://eutils.ncbi.nlm.nih.gov/soap/v2.0/eutils.wsdl run_eSearch net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 5 net.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.Retry 1.0 1000 5000 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokerun_eSearch_requestdb0rettype0term0mindate0maxdate0output00net.sf.taverna.t2.activitieswsdl-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity db 0 'text/plain' false term 0 'text/plain' false WebEnv 0 'text/plain' false QueryKey 0 'text/plain' false usehistory 0 'text/plain' false tool 0 'text/plain' false email 0 'text/plain' false field 0 'text/plain' false reldate 0 'text/plain' false mindate 0 'text/plain' false maxdate 0 'text/plain' false datetype 0 'text/plain' false RetStart 0 'text/plain' false RetMax 0 'text/plain' false rettype 0 'text/plain' false sort 0 'text/plain' false output 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="eSearchRequest" name="request" 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.ncbi.nlm.nih.gov/soap/eutils/esearch}&gt;eSearchRequest&gt;db" /><s:basetype optional="true" unbounded="false" typename="string" name="term" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/esearch}&gt;eSearchRequest&gt;term" /><s:basetype optional="true" unbounded="false" typename="string" name="WebEnv" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/esearch}&gt;eSearchRequest&gt;WebEnv" /><s:basetype optional="true" unbounded="false" typename="string" name="QueryKey" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/esearch}&gt;eSearchRequest&gt;QueryKey" /><s:basetype optional="true" unbounded="false" typename="string" name="usehistory" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/esearch}&gt;eSearchRequest&gt;usehistory" /><s:basetype optional="true" unbounded="false" typename="string" name="tool" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/esearch}&gt;eSearchRequest&gt;tool" /><s:basetype optional="true" unbounded="false" typename="string" name="email" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/esearch}&gt;eSearchRequest&gt;email" /><s:basetype optional="true" unbounded="false" typename="string" name="field" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/esearch}&gt;eSearchRequest&gt;field" /><s:basetype optional="true" unbounded="false" typename="string" name="reldate" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/esearch}&gt;eSearchRequest&gt;reldate" /><s:basetype optional="true" unbounded="false" typename="string" name="mindate" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/esearch}&gt;eSearchRequest&gt;mindate" /><s:basetype optional="true" unbounded="false" typename="string" name="maxdate" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/esearch}&gt;eSearchRequest&gt;maxdate" /><s:basetype optional="true" unbounded="false" typename="string" name="datetype" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/esearch}&gt;eSearchRequest&gt;datetype" /><s:basetype optional="true" unbounded="false" typename="string" name="RetStart" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/esearch}&gt;eSearchRequest&gt;RetStart" /><s:basetype optional="true" unbounded="false" typename="string" name="RetMax" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/esearch}&gt;eSearchRequest&gt;RetMax" /><s:basetype optional="true" unbounded="false" typename="string" name="rettype" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/esearch}&gt;eSearchRequest&gt;rettype" /><s:basetype optional="true" unbounded="false" typename="string" name="sort" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/esearch}&gt;eSearchRequest&gt;sort" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.StringConstantActivity 500 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.WSDLActivity http://projects.biotec.tu-dresden.de/DOG4DAG_TAVERNA/services/GoPubMedTermGeneration?wsdl generateTerminology net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.XMLInputSplitterActivity applicationCode 0 'text/plain' false texts 1 l('text/plain') false maxNumberOfTerms 0 'text/plain' false output 0 '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}&gt;generateTerminology&gt;applicationCode" /><s:arraytype optional="true" unbounded="true" wrapped="false" typename="string" name="texts" qname="{http://server.gopubmedTermGenerationService.biotec.tud.de}&gt;generateTerminology&gt;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}&gt;generateTerminology&gt;maxNumberOfTerms" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.StringConstantActivity 20110209_taverna net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeremove_nullsinputgene_and_abstractoutputgene_and_abstractabstractsSearch_PubMedconcat_datagene_and_abstractpathwaysplit_search_termssplitsplit_search_termsregexregexvaluesplit_search_termsstringremove_Nulls_2outputmerge_outputs_2stringlistclean_textcleaned_textSearch_PubMedsearch_termsplit_search_termssplitSearch_PubMedmin_datemin_datevalueSearch_PubMedmax_datemax_datevalueSearch_PubMedmax_returnmax_return_genevalueclean_textinputremove_nullsoutputRemove_duplicate_genesstringlistsplit_gene_namessplitsplit_gene_namesstringgene_namessplit_gene_namesregexregular_expressionvalueremove_Nulls_2inputMerge_string_list_to_stringconcatenatedMerge_string_list_to_stringstringlistRemove_duplicate_genesstrippedlistrun_eSearchparametersparametersXML_eSearchoutputextractPMIDxpathxpathvalueextractPMIDxml-textrun_eSearchparametersremove_Nulls_4inputmerge_phenotype_abstractsoutputconcat_abstract_idsidextractPMIDnodelistconcat_abstract_idsabstract_textmerge_abstractsconcatenatedconcat_abstract_idsdate_textmerge_datesconcatenatedmerge_phenotype_abstractsabstractsmerge_abstract_idsconcatenatedmerge_phenotype_abstractsphenotypePhenotype_search_termmerge_abstractsstringlistFetch_AbstractsabstractsparametersXML_eSearchRetMaxmax_return_phenotypevalueparametersXML_eSearchdbpubmed_databasevalueparametersXML_eSearchmaxdatemax_datevalueparametersXML_eSearchmindatemin_datevalueparametersXML_eSearchtermPhenotype_search_termmerge_abstract_idsstringlistconcat_abstract_idsoutputmerge_datesstringlistFetch_Abstractspubmed_datesFetch_Abstractspubmed_idsextractPMIDnodelistclean_text_3inputremove_Nulls_4outputEncode_byte_to_base64bytesclean_text_3cleaned_textmerge_strings_2stringlistmerge_stringsconcatenatedextract_abstractsinputclean_text_4outputmerge_search_and_termstermsmerge_strings_2concatenatedmerge_search_and_termssearch_termextract_abstractsoutput_searchextract_Terms_2xpathxpath_2valueextract_Terms_2xml-textgenerateTerminologyparametersmerge_stringsstringlistRemove_duplicate_strings_2strippedlistremove_Nulls_5inputmerge_search_and_termsoutputRemove_duplicate_strings_2stringlistextract_Terms_2nodelistsplit_by_regexregexregex_3valuesplit_by_regexstringextract_abstractsoutputclean_text_4file_direct_dataEncode_byte_to_base64base64extract_terms_3inputremove_Nulls_5outputmerge_term_counttermsplit_extracted_termssplitmerge_term_countcountmerge_extractedconcatenatedsplit_extracted_termsstringextract_terms_3outputsplit_extracted_termsregexregular_expression_2valuemerge_pubmed_countstringlistextractCountnodelistmerge_extractedstringlistextractCount_2nodelistmerge_liststringlistmerge_term_countoutputextractCount_2xpathxpath_3valueextractCount_2xml-textrun_eSearch_2resultextractCountxpathxpath_countvalueextractCountxml-textrun_eInforesultparametersXML_1dbpubmed_database_2valuerun_eInforequestparametersXML_1outputrun_eSearch_2requestrun_eSearch_requestoutputrun_eSearch_requestdbeSearch_databasevaluerun_eSearch_requestrettypecountvaluerun_eSearch_requesttermsplit_extracted_termssplitrun_eSearch_requestmindatemin_datevaluerun_eSearch_requestmaxdatemax_datevalueGENE_RankPhenotypeTermspubmed_abstract_numbermerge_pubmed_countconcatenatedGENE_RankPhenotypeTermsphenotype_term_countsmerge_listconcatenatedGENE_RankPhenotypeTermsquery_abstractsmerge_outputs_2concatenatedGENE_RankPhenotypeTermsphenotype_abstractsclean_text_3cleaned_textGENE_RankPhenotypeTermsphenotype_termsremove_Nulls_5outputgenerateTerminologyparametersgenerateTerminology_inputoutputgenerateTerminology_inputtextssplit_by_regexsplitgenerateTerminology_inputapplicationCodeapplicationCode_valuevaluegene_abstractsmerge_outputs_2concatenatedphenotype_abstractsclean_text_3cleaned_textphenotype_termsremove_Nulls_5outputphenotype_term_countsmerge_listconcatenatedpubmed_abstract_numbermerge_pubmed_countconcatenatedgene_cosineGENE_RankPhenotypeTermscosine_vector_scoresgene_term_enrichment_scoresGENE_RankPhenotypeTermsconcept_rankings cca35e36-81ae-464c-b04b-335af69bf3b3 2011-02-08 12:57:23.600 GMT 1e8b87f0-d733-4fc2-b9d7-458264d5f70d 2011-02-10 16:00:14.408 GMT a1f6f265-068a-46ee-8966-36e3abb4ebe4 2011-02-02 15:23:46.908 GMT 5efb1e8b-e09e-4de8-8cab-a7352a0c2bb6 2011-02-03 13:17:30.347 GMT 2964ebe6-e008-408e-ab98-08eb239fc6d0 2011-02-08 13:05:26.360 GMT 411c7f97-71ea-4efc-9832-3d244cea610b 2011-01-11 11:53:58.134 GMT 630d0538-a24f-4b45-9132-dbd7931aad9f 2011-02-02 15:20:31.627 GMT 15af69a6-9f6e-4da4-8e54-7c5d6c4b7e2c 2011-02-03 18:21:58.815 GMT 472ec8c8-9b6c-4921-ad61-cbfcba71aa57 2011-02-04 14:05:40.76 GMT c6b7062b-3107-4a49-9dca-8e2ab6b87fd7 2010-12-24 16:32:58.894 GMT Paul Fisher 2010-12-24 16:25:11.10 GMT d5e42d7e-cfc2-4b8e-a7be-94d5308b379f 2011-02-02 15:37:20.162 GMT c660e6ba-63d5-4b3b-a8c5-f5366b198332 2011-02-08 13:10:22.904 GMT 044c19bb-f91a-472d-8c76-f77138099377 2011-02-08 16:04:15.243 GMT 37b26ab0-b32f-4cc5-99a1-0397999e8603 2011-02-04 13:07:47.695 GMT ef82e651-933b-4c7e-81b8-2d4c3404ec63 2011-01-11 16:37:06.276 GMT Gene to Pubmed 2010-12-24 16:25:11.10 GMT cfd5b48e-ecdb-492f-a4c7-d15410015313 2010-12-27 17:24:27.435 GMT 02b8d6bf-666d-4e32-ac76-ba0061020f15 2011-02-03 12:54:56.337 GMT 02b50687-d057-4b5e-99fd-a1ed4fdef4a9 2010-12-24 16:34:14.73 GMT 21542038-b8c9-41da-bbc8-62d7afdcff09 2010-12-24 16:35:46.602 GMT 092666c7-cffc-4b88-b53a-0aaaa37037fa 2011-02-08 12:37:26.587 GMT This 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 GMT clean_textinput00 text/plain 2010-12-27 17:24:06.126 GMT 2010-12-27 17:24:06.126 GMT cleaned_textclean_textfile_direct_data0report00output00net.sf.taverna.t2.activitiessoaplab-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.soaplab.SoaplabActivity http://phoebus.cs.man.ac.uk:1977/axis/services/text_mining.clean_text 0 1.0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.BeanshellActivity string 0 'text/plain' java.lang.String true bytes 0 'application/octet-stream' 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.LocalworkerActivity bytes 0 'application/octet-stream' [B true base64 0 'text/plain' 0 workflow commons-codec commons-codec 1.3 1635363350 commons-codec:commons-codec:1.3 org.embl.ebi.escience.scuflworkers.java.EncodeBase64 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeclean_textfile_direct_dataEncode_byte___to_base64base64stringToBytesstringinputEncode_byte___to_base64bytesstringToBytesbytescleaned_textclean_textoutput 2010-12-27 17:24:06.438 GMT clean_text 2010-12-27 17:24:06.438 GMT 2010-12-27 17:24:06.438 GMT 1d592ca5-aba5-4bf5-b657-bd90702f9186 2010-12-27 17:24:06.578 GMT XPathPubmedIdspubmed_ids00 2010-12-24 16:25:10.417 GMT text/plain 2010-12-24 16:25:10.417 GMT abstract text/plain 2010-12-24 16:25:10.417 GMT date text/plain 2010-12-24 16:25:10.418 GMT xpathvalue00net.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.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.WSDLActivity http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/efetch_pubmed.wsdl run_eFetch net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 5 net.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.LocalworkerActivity xpath 0 'text/plain' java.lang.String true xml-text 0 'text/xml' java.lang.String true nodelist 1 l('text/plain') 1 nodelistAsXML 1 l('text/plain') 1 workflow dom4j dom4j 1.6 716010169 dom4j:dom4j:1.6 net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.LocalworkerActivity xpath 0 'text/plain' java.lang.String true xml-text 0 'text/xml' java.lang.String true nodelist 1 l('text/plain') 1 nodelistAsXML 1 l('text/plain') 1 workflow dom4j dom4j 1.6 716010169 dom4j:dom4j:1.6 net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.XMLInputSplitterActivity id 0 'text/plain' java.lang.String true WebEnv 0 'text/plain' java.lang.String true query_key 0 'text/plain' java.lang.String true tool 0 'text/plain' java.lang.String true email 0 'text/plain' java.lang.String true retstart 0 'text/plain' java.lang.String true retmax 0 'text/plain' java.lang.String true rettype 0 'text/plain' java.lang.String true output 0 'text/xml' 0 <s:extensions 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}&gt;eFetchRequest&gt;id" /><s:basetype optional="true" unbounded="false" typename="string" name="WebEnv" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch_pubmed}&gt;eFetchRequest&gt;WebEnv" /><s:basetype optional="true" unbounded="false" typename="string" name="query_key" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch_pubmed}&gt;eFetchRequest&gt;query_key" /><s:basetype optional="true" unbounded="false" typename="string" name="tool" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch_pubmed}&gt;eFetchRequest&gt;tool" /><s:basetype optional="true" unbounded="false" typename="string" name="email" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch_pubmed}&gt;eFetchRequest&gt;email" /><s:basetype optional="true" unbounded="false" typename="string" name="retstart" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch_pubmed}&gt;eFetchRequest&gt;retstart" /><s:basetype optional="true" unbounded="false" typename="string" name="retmax" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch_pubmed}&gt;eFetchRequest&gt;retmax" /><s:basetype optional="true" unbounded="false" typename="string" name="rettype" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch_pubmed}&gt;eFetchRequest&gt;rettype" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokerun_eFetchinppinppXMLoutputextractDatesxml-textrun_eFetchoutpextractDatesxpathxpath_2valueextractAbstractxml-textrun_eFetchoutpextractAbstractxpathxpathvalueinppXMLidpubmed_idsabstractextractAbstractnodelistdateextractDatesnodelist 0e12e023-764d-4bf0-a829-2d7e97d876e0 2010-12-24 16:35:09.315 GMT This 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 GMT XPath Pubmed Ids 2010-12-24 16:25:11.6 GMT Paul Fisher 2010-12-24 16:25:11.6 GMT 5cea1753-adae-440d-b871-876d38b84ff6 2010-12-24 16:26:20.146 GMT RankPhenotypeTermsphenotype_terms00 2010-12-25 19:50:04.935 GMT phenotype_abstracts00 2010-12-25 19:50:04.935 GMT text/plain 2010-12-25 19:50:04.935 GMT query_abstracts00 2010-12-25 19:50:04.935 GMT text/plain 2010-12-25 19:50:04.935 GMT phenotype_term_counts00pubmed_abstract_number00concept_rankings text/plain 2010-12-25 19:50:04.951 GMT cosine_vector_scorestwo_newlinesvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity \n\n net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesplit_abstracts_by_regexregex0string0split11net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivity string 0 'text/plain' java.lang.String true regex 0 'text/plain' java.lang.String true split 1 l('text/plain') 1 workflow org.embl.ebi.escience.scuflworkers.java.SplitByRegex net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokecosine_vector_spacepathway_abstracts_direct_data0phenotype_terms_direct_data0phenotype_term_count_direct_data0report00output00net.sf.taverna.t2.activitiessoaplab-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.soaplab.SoaplabActivity http://phoebus.cs.man.ac.uk:1977/axis/services/text_mining.cosine_vector_space 0 1.0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemerge_cosine_scoresstringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true seperator 0 'text/plain' java.lang.String true concatenated 0 'text/plain' 0 workflow org.embl.ebi.escience.scuflworkers.java.StringListMerge net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeenriched_pathwayphenotype_terms_direct_data0pathway_abstracts_direct_data0pubmed_count_direct_data0term_count_direct_data0report00output00net.sf.taverna.t2.activitiessoaplab-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.soaplab.SoaplabActivity http://phoebus.cs.man.ac.uk:1977/axis/services/text_mining.enriched_pathway 0 1.0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeenriched_phenotypephenotype_abstract_direct_data0phenotype_terms_direct_data0term_count_direct_data0pubmed_count_direct_data0report00output00net.sf.taverna.t2.activitiessoaplab-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.soaplab.SoaplabActivity http://phoebus.cs.man.ac.uk:1977/axis/services/text_mining.enriched_phenotype 0 1.0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokecalculate_linksenriched_pathway_direct_data0enriched_phenotype_direct_data0report00output00net.sf.taverna.t2.activitiessoaplab-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.soaplab.SoaplabActivity http://phoebus.cs.man.ac.uk:1977/axis/services/text_mining.calculate_links 0 1.0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeformat_rankingsranked_terms0title_term_rankings00net.sf.taverna.t2.activitiesbeanshell-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivity ranked_terms 0 'text/plain' java.lang.String true title_term_rankings 0 'text/plain' 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemerge_format_rankingsstringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true seperator 0 'text/plain' java.lang.String true concatenated 0 'text/plain' 0 workflow org.embl.ebi.escience.scuflworkers.java.StringListMerge net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.BeanshellActivity input 0 'text/plain' java.lang.String true output 0 'text/plain' 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesplit_abstracts_by_regexregextwo_newlinesvaluesplit_abstracts_by_regexstringquery_abstractscosine_vector_spacepathway_abstracts_direct_datasplit_abstracts_by_regexsplitcosine_vector_spacephenotype_terms_direct_dataphenotype_termscosine_vector_spacephenotype_term_count_direct_dataphenotype_term_countsmerge_cosine_scoresstringlistcosine_vector_spaceoutputenriched_pathwayphenotype_terms_direct_dataphenotype_termsenriched_pathwaypathway_abstracts_direct_datasplit_abstracts_by_regexsplitenriched_pathwaypubmed_count_direct_datapubmed_abstract_numberenriched_pathwayterm_count_direct_dataphenotype_term_countsenriched_phenotypephenotype_abstract_direct_dataphenotype_abstractsenriched_phenotypephenotype_terms_direct_dataphenotype_termsenriched_phenotypeterm_count_direct_dataphenotype_term_countsenriched_phenotypepubmed_count_direct_datapubmed_abstract_numbercalculate_linksenriched_pathway_direct_dataenriched_pathwayoutputcalculate_linksenriched_phenotype_direct_dataenriched_phenotypeoutputformat_rankingsranked_termscalculate_linksoutputmerge_format_rankingsstringlistformat_rankingstitle_term_rankingsremove_Nullsinputmerge_cosine_scoresconcatenatedconcept_rankingsmerge_format_rankingsconcatenatedcosine_vector_scoresremove_Nullsoutput ac1f2dc2-f9a9-4c74-86ff-377b00f15710 2011-02-01 11:17:52.110 GMT cc5d8438-319a-4327-9261-c2752656150c 2011-01-31 13:10:30.83 GMT 7ce75b2a-baa5-4231-8ded-7a763e6cd69c 2011-02-04 13:07:45.14 GMT This 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 GMT 9f53e57c-a222-49e1-ae05-bae6e891dac9 2010-12-25 19:55:34.403 GMT 97d23587-e50d-4926-b62e-2becaded5c60 2010-12-27 14:55:31.822 GMT e27c607d-a2ff-405a-9fb1-c33f4c543d7e 2010-12-26 12:29:03.697 GMT 79bcd1ec-38a6-4634-8eea-21a1edc3e34b 2010-12-25 19:59:38.23 GMT 38f5f9ed-2361-431b-bcc4-e74131eec66a 2011-01-31 13:08:42.909 GMT Paul Fisher 2010-12-25 19:50:14.124 GMT 979cf52b-1f9a-4be2-9cda-50552b6ec0bd 2010-12-25 19:51:05.480 GMT 0f3ee5e9-60b7-43c4-b940-4bc2482c85e0 2010-12-27 15:03:30.135 GMT 16ad416d-9049-42ce-a263-8d28ed90e6d4 2010-12-27 14:49:02.865 GMT bed0ff14-4766-41bb-a15d-f1d6bf98cc4d 2010-12-27 15:05:03.812 GMT 9ddd20a9-4d5b-4fec-bd5b-a045741f11de 2011-02-02 15:14:54.159 GMT This 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 GMT Rank Phenotype Terms 2010-12-25 19:50:14.124 GMT 87e7ef54-f110-4027-9765-9d0a837efb2a 2011-02-02 15:05:20.786 GMT XPathPubmedIdspubmed_ids00 text/plain 2010-12-24 17:14:54.310 GMT 2010-12-24 17:14:54.310 GMT pubmed_dates text/plain 2010-12-24 17:14:54.310 GMT abstracts text/plain 2010-12-24 17:14:54.310 GMT xpath2value00net.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.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.LocalworkerActivity xpath 0 'text/plain' java.lang.String true xml-text 0 'text/xml' java.lang.String true nodelist 1 l('text/plain') 1 nodelistAsXML 1 l('text/plain') 1 workflow dom4j dom4j 1.6 716010169 dom4j:dom4j:1.6 net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.XMLInputSplitterActivity db 0 'text/plain' java.lang.String true id 0 'text/plain' java.lang.String true WebEnv 0 'text/plain' java.lang.String true query_key 0 'text/plain' java.lang.String true tool 0 'text/plain' java.lang.String true email 0 'text/plain' java.lang.String true retstart 0 'text/plain' java.lang.String true retmax 0 'text/plain' java.lang.String true rettype 0 'text/plain' java.lang.String true strand 0 'text/plain' java.lang.String true seq_start 0 'text/plain' java.lang.String true seq_stop 0 'text/plain' java.lang.String true complexity 0 'text/plain' java.lang.String true report 0 'text/plain' java.lang.String true output 0 '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}&gt;eFetchRequest&gt;db" /><s:basetype optional="true" unbounded="false" typename="string" name="id" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}&gt;eFetchRequest&gt;id" /><s:basetype optional="true" unbounded="false" typename="string" name="WebEnv" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}&gt;eFetchRequest&gt;WebEnv" /><s:basetype optional="true" unbounded="false" typename="string" name="query_key" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}&gt;eFetchRequest&gt;query_key" /><s:basetype optional="true" unbounded="false" typename="string" name="tool" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}&gt;eFetchRequest&gt;tool" /><s:basetype optional="true" unbounded="false" typename="string" name="email" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}&gt;eFetchRequest&gt;email" /><s:basetype optional="true" unbounded="false" typename="string" name="retstart" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}&gt;eFetchRequest&gt;retstart" /><s:basetype optional="true" unbounded="false" typename="string" name="retmax" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}&gt;eFetchRequest&gt;retmax" /><s:basetype optional="true" unbounded="false" typename="string" name="rettype" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}&gt;eFetchRequest&gt;rettype" /><s:basetype optional="true" unbounded="false" typename="string" name="strand" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}&gt;eFetchRequest&gt;strand" /><s:basetype optional="true" unbounded="false" typename="string" name="seq_start" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}&gt;eFetchRequest&gt;seq_start" /><s:basetype optional="true" unbounded="false" typename="string" name="seq_stop" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}&gt;eFetchRequest&gt;seq_stop" /><s:basetype optional="true" unbounded="false" typename="string" name="complexity" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}&gt;eFetchRequest&gt;complexity" /><s:basetype optional="true" unbounded="false" typename="string" name="report" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}&gt;eFetchRequest&gt;report" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.StringConstantActivity pubmed net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.LocalworkerActivity xpath 0 'text/plain' java.lang.String true xml-text 0 'text/xml' java.lang.String true nodelist 1 l('text/plain') 1 nodelistAsXML 1 l('text/plain') 1 workflow dom4j dom4j 1.6 716010169 dom4j:dom4j:1.6 net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.WSDLActivity http://eutils.ncbi.nlm.nih.gov/soap/v2.0/efetch_pubmed.wsdl run_eFetch net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 5 net.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.Retry 1.0 1000 5000 5 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeextractAbstractxpathxpathvalueextractAbstractxml-textrun_eFetchoutpparametersXMLidpubmed_idsparametersXMLdbdatabasevalueextractDatesxpathxpath2valueextractDatesxml-textrun_eFetchoutprun_eFetchinppparametersXMLoutputpubmed_datesextractDatesnodelistabstractsextractAbstractnodelist fa9e3c15-b654-4364-b0ce-dd4f1bab3f6f 2010-12-24 17:36:31.757 GMT This 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 GMT 0d5a76a5-82c8-4719-9b78-afa89256efca 2010-12-24 17:17:15.417 GMT Paul Fisher 2010-12-24 17:14:54.640 GMT XPath Pubmed Ids 2010-12-24 17:14:54.640 GMT clean_textinput00 text/plain 2010-12-27 17:24:56.320 GMT 2010-12-27 17:24:56.320 GMT cleaned_textEncode_byte___to_base64bytes0base6400net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivity bytes 0 'application/octet-stream' [B true base64 0 'text/plain' 0 workflow commons-codec commons-codec 1.3 1635363350 commons-codec:commons-codec:1.3 org.embl.ebi.escience.scuflworkers.java.EncodeBase64 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeclean_textfile_direct_data0report00output00net.sf.taverna.t2.activitiessoaplab-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.soaplab.SoaplabActivity http://phoebus.cs.man.ac.uk:1977/axis/services/text_mining.clean_text 0 1.0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.BeanshellActivity string 0 'text/plain' java.lang.String true bytes 0 'application/octet-stream' 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeEncode_byte___to_base64bytesstringToBytesbytesclean_textfile_direct_dataEncode_byte___to_base64base64stringToBytesstringinputcleaned_textclean_textoutput 52829fcd-29cd-4a65-a3a7-582f6b6376de 2010-12-27 17:24:56.804 GMT clean_text 2010-12-27 17:24:56.632 GMT 2010-12-27 17:24:56.632 GMT 2010-12-27 17:24:56.632 GMT PathwaytoPubMedsearch_term00 2010-12-24 16:25:09.726 GMT text/plain 2010-12-24 16:25:09.726 GMT min_date00max_date00max_return00concat_data text/plain 2010-12-24 16:25:09.726 GMT pubmed_databasevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity pubmed net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeconcat_abstract_idsdate_text0abstract_text0id0output00net.sf.taverna.t2.activitiesbeanshell-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivity id 0 'text/plain' java.lang.String true abstract_text 0 'text/plain' java.lang.String true date_text 0 'text/plain' java.lang.String true output 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.WSDLActivity http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl run_eSearch net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true seperator 0 'text/plain' java.lang.String true concatenated 0 'text/plain' 0 workflow org.embl.ebi.escience.scuflworkers.java.StringListMerge net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true seperator 0 'text/plain' java.lang.String true concatenated 0 'text/plain' 0 workflow org.embl.ebi.escience.scuflworkers.java.StringListMerge net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true seperator 0 'text/plain' java.lang.String true concatenated 0 'text/plain' 0 workflow org.embl.ebi.escience.scuflworkers.java.StringListMerge net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.LocalworkerActivity xpath 0 'text/plain' java.lang.String true xml-text 0 'text/xml' java.lang.String true nodelist 1 l('text/plain') 1 nodelistAsXML 1 l('text/plain') 1 workflow dom4j dom4j 1.6 716010169 dom4j:dom4j:1.6 net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeparametersXML_eFecthterm0db0RetMax0maxdate0mindate0output00net.sf.taverna.t2.activitieswsdl-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity db 0 'text/plain' java.lang.String true term 0 'text/plain' java.lang.String true WebEnv 0 'text/plain' java.lang.String true QueryKey 0 'text/plain' java.lang.String true usehistory 0 'text/plain' java.lang.String true tool 0 'text/plain' java.lang.String true email 0 'text/plain' java.lang.String true field 0 'text/plain' java.lang.String true reldate 0 'text/plain' java.lang.String true mindate 0 'text/plain' java.lang.String true maxdate 0 'text/plain' java.lang.String true datetype 0 'text/plain' java.lang.String true RetStart 0 'text/plain' java.lang.String true RetMax 0 'text/plain' java.lang.String true rettype 0 'text/plain' java.lang.String true sort 0 'text/plain' java.lang.String true output 0 '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.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.Parallelize 5 net.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.Retry 1.0 1000 5000 5 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeconcat_abstract_idsdate_textmerge_datesconcatenatedconcat_abstract_idsabstract_textmerge_abstractsconcatenatedconcat_abstract_idsidextractPMIDnodelistrun_eSearchparametersparametersXML_eFecthoutputmerge_datesstringlistRetrive_abstractsdatemerge_abstract_idsstringlistconcat_abstract_idsoutputmerge_abstractsstringlistRetrive_abstractsabstractextractPMIDxml-textrun_eSearchparametersextractPMIDxpathxpathvalueparametersXML_eFecthtermsearch_termparametersXML_eFecthdbpubmed_databasevalueparametersXML_eFecthRetMaxmax_returnparametersXML_eFecthmaxdatemax_dateparametersXML_eFecthmindatemin_dateRetrive_abstractspubmed_idsextractPMIDnodelistconcat_datamerge_abstract_idsconcatenated Paul Fisher 2010-12-24 16:25:11.9 GMT a1afe21b-b3e9-4f41-8de4-5910263a75df 2010-12-24 16:26:19.779 GMT 968d2b6b-54ce-499a-9748-2e1f8d3b64b2 2010-12-24 16:35:34.138 GMT b284797f-907b-494b-be67-0a922a30a74d 2011-02-02 15:23:00.575 GMT 685e516d-282a-4921-96f0-5bdf6dad3c7c 2010-12-24 16:34:03.113 GMT This 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 user 2010-12-24 16:25:11.9 GMT Pathway to PubMed 2010-12-24 16:25:11.9 GMT