Workflow1gene_ids00pathway_descriptionscompound_idspathway_abstractsNested_workflowkegg_pathway_id_list0pathway_descriptions00net.sf.taverna.t2.activitiesdataflow-activity1.0.1net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeNested_workflow_2pathway_descriptions0pathway_abstracts00net.sf.taverna.t2.activitiesdataflow-activity1.0.1net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeget_compounds_by_pathwaypathway_id0return11net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://soap.genome.jp/KEGG.wsdl get_compounds_by_pathway net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeget_pathways_by_genesgenes_id_list1return11net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://soap.genome.jp/KEGG.wsdl get_pathways_by_genes net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeNested_workflowkegg_pathway_id_listget_pathways_by_genesreturnNested_workflow_2pathway_descriptionsNested_workflowpathway_descriptionsget_compounds_by_pathwaypathway_idget_pathways_by_genesreturnget_pathways_by_genesgenes_id_listgene_idspathway_descriptionsNested_workflowpathway_descriptionscompound_idsget_compounds_by_pathwayreturnpathway_abstractsNested_workflow_2pathway_abstractsPathwaytoPubmedpathway_descriptions00 2010-03-10 18:39:07.476 GMT text/plain 2010-03-10 18:39:07.466 GMT pathway_abstracts text/plain 2010-03-10 18:39:07.476 GMT regexvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivity \n net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeremove_nullsinput0output00net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true input 0 'text/plain' 0 output 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokepathway_and_abstractpathway0abstracts0output00net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true pathway 0 'text/plain' java.lang.String true abstracts 0 'text/plain' 0 output 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeextract_termsinput0output00net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true input 0 'text/plain' 0 output 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeadd_MeSH_to_stringinput0output00net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true input 0 'text/plain' 0 output 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemerge_outputs_2stringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.StringListMerge workflow java.lang.String true stringlist 1 l('text/plain') java.lang.String true seperator 0 'text/plain' 0 concatenated 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesplit_search_termsregex0string0split11net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.SplitByRegex workflow java.lang.String true string 0 'text/plain' java.lang.String true regex 0 'text/plain' 1 split 1 l('text/plain') net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeNested_WorkflowPathway_search_term0concat_data00net.sf.taverna.t2.activitiesdataflow-activity1.0.1net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeremove_nullsinputpathway_and_abstractoutputpathway_and_abstractpathwaysplit_search_termssplitpathway_and_abstractabstractsNested_Workflowconcat_dataextract_termsinputpathway_descriptionsadd_MeSH_to_stringinputextract_termsoutputmerge_outputs_2stringlistremove_nullsoutputsplit_search_termsregexregexvaluesplit_search_termsstringadd_MeSH_to_stringoutputNested_WorkflowPathway_search_termsplit_search_termssplitpathway_abstractsmerge_outputs_2concatenated Paul Fisher 2010-03-10 18:39:09.356 GMT Pathway to Pubmed 2010-03-10 18:39:09.356 GMT This workflow takes in a list of KEGG pathway descriptions and searches the PubMed database for corresponding articles. Any matches to the pathways are then retrieved (abstracts only). These abstracts are then returned to the user. 2010-03-10 18:39:09.356 GMT Get_Kegg_Pathway_informationkegg_pathway_id_list00 text/plain 2010-03-10 16:48:48.46 GMT 2010-03-10 16:48:48.48 GMT pathway_descriptions text/plain 2010-03-10 16:48:48.52 GMT remove_Nullsinput0output00net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true input 0 'text/plain' 0 output 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemerge_descriptionsstringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.StringListMerge workflow java.lang.String true stringlist 1 l('text/plain') java.lang.String true seperator 0 'text/plain' 0 concatenated 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokebtitstring0return00attachmentList11net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://soap.genome.jp/KEGG.wsdl btit net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregexvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivity \n net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesplit_by_regexregex0string0split11net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.SplitByRegex workflow java.lang.String true string 0 'text/plain' java.lang.String true regex 0 'text/plain' 1 split 1 l('text/plain') net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeremove_Nullsinputmerge_descriptionsconcatenatedmerge_descriptionsstringlistbtitreturnbtitstringsplit_by_regexsplitsplit_by_regexregexregexvaluesplit_by_regexstringkegg_pathway_id_listpathway_descriptionsremove_Nullsoutput Get Kegg Gene information 2010-03-10 16:48:49.21 GMT This workflow gets a series of information relating to a list of KEGG pathways supplied to it. It also removes any null values from a list of strings. Example input: 2010-03-10 17:02:28.283 GMT Get Kegg Pathway information 2010-03-10 17:01:54.792 GMT This workflow gets a series of information relating to a list of KEGG pathways supplied to it. It also removes any null values from a list of strings. 2010-03-10 17:01:59.68 GMT This workflow gets a series of information relating to a list of KEGG genes supplied to it. It also removes any null values from a list of strings. 2010-03-10 16:48:49.21 GMT This workflow gets a series of information relating to a list of KEGG pathways supplied to it. It also removes any null values from a list of strings. Example input: path:mmu04010 path:mmu05014 2010-03-10 17:14:21.387 GMT Paul Fisher 2010-03-10 16:48:49.21 GMT This workflow gets a series of information relating to a list of KEGG pathways supplied to it. It also removes any null values from a list of strings. Example input: mmu04010 mmu05014 2010-03-10 17:03:12.221 GMT XPathPubmedIdspubmed_ids00 text/plain 2010-03-10 18:39:09.286 GMT 2010-03-10 18:39:09.286 GMT abstract text/plain 2010-03-10 18:39:09.286 GMT date text/plain 2010-03-10 18:39:09.286 GMT databasevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivity pubmed net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokexpathvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.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-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokexpath_2value00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.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-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeextractAbstractxml-text0xpath0nodelistAsXML11nodelist11net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivity net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker dom4j:dom4j:1.6 workflow dom4j dom4j 1.6 716010169 java.lang.String true xpath 0 'text/plain' java.lang.String true xml-text 0 'text/xml' 1 nodelist 1 l('text/plain') 1 nodelistAsXML 1 l('text/plain') net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeextractDatesxml-text0xpath0nodelistAsXML11nodelist11net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivity net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker dom4j:dom4j:1.6 workflow dom4j dom4j 1.6 716010169 java.lang.String true xpath 0 'text/plain' java.lang.String true xml-text 0 'text/xml' 1 nodelist 1 l('text/plain') 1 nodelistAsXML 1 l('text/plain') net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeparametersXMLid0db0output00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="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> java.lang.String true 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' 0 output 0 'text/xml' net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokerun_eFetchparameters0attachmentList11parameters00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl run_eFetch net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeextractAbstractxml-textrun_eFetchparametersextractAbstractxpathxpathvalueextractDatesxml-textrun_eFetchparametersextractDatesxpathxpath_2valueparametersXMLidpubmed_idsparametersXMLdbdatabasevaluerun_eFetchparametersparametersXMLoutputabstractextractAbstractnodelistdateextractDatesnodelist Paul Fisher 2010-03-10 18:39:09.356 GMT XPath Pubmed Ids 2010-03-10 18:39:09.356 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. 2010-03-10 18:39:09.356 GMT PathwaytoPubMedPathway_search_term00 text/plain 2010-03-10 18:39:09.166 GMT 2010-03-10 18:39:09.166 GMT concat_data text/plain 2010-03-10 18:39:09.166 GMT max_returnvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivity 500 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemerge_abstract_idsstringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.StringListMerge workflow java.lang.String true stringlist 1 l('text/plain') java.lang.String true seperator 0 'text/plain' 0 concatenated 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokepubmed_databasevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivity pubmed net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeextractPMIDxml-text0xpath0nodelistAsXML11nodelist11net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivity net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker dom4j:dom4j:1.6 workflow dom4j dom4j 1.6 716010169 java.lang.String true xpath 0 'text/plain' java.lang.String true xml-text 0 'text/xml' 1 nodelist 1 l('text/plain') 1 nodelistAsXML 1 l('text/plain') net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeend_datevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivity 2008/12/31 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemerge_datesstringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.StringListMerge workflow java.lang.String true stringlist 1 l('text/plain') java.lang.String true seperator 0 'text/plain' 0 concatenated 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokexpathvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivity /*[local-name(.)='eSearchResult']/*[local-name(.)='IdList']/*[local-name(.)='Id'] net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeconcat_abstract_idsid0abstract_text0date_text0output00net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true id 0 'text/plain' java.lang.String true abstract_text 0 'text/plain' java.lang.String true date_text 0 'text/plain' 0 output 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokerun_eSearchparameters0attachmentList11parameters00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl run_eSearch net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeparametersXML_eFecthmaxdate0RetMax0db0term0mindate0output00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="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> java.lang.String true 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' 0 output 0 'text/xml' net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokestart_datevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivity 2005/01/01 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemerge_abstractsstringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.StringListMerge workflow java.lang.String true stringlist 1 l('text/plain') java.lang.String true seperator 0 'text/plain' 0 concatenated 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRetrive_abstractspubmed_ids0date11abstract11net.sf.taverna.t2.activitiesdataflow-activity1.0.1net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemerge_abstract_idsstringlistconcat_abstract_idsoutputextractPMIDxml-textrun_eSearchparametersextractPMIDxpathxpathvaluemerge_datesstringlistRetrive_abstractsdateconcat_abstract_idsidextractPMIDnodelistconcat_abstract_idsabstract_textmerge_abstractsconcatenatedconcat_abstract_idsdate_textmerge_datesconcatenatedrun_eSearchparametersparametersXML_eFecthoutputparametersXML_eFecthmaxdateend_datevalueparametersXML_eFecthRetMaxmax_returnvalueparametersXML_eFecthdbpubmed_databasevalueparametersXML_eFecthtermPathway_search_termparametersXML_eFecthmindatestart_datevaluemerge_abstractsstringlistRetrive_abstractsabstractRetrive_abstractspubmed_idsextractPMIDnodelistconcat_datamerge_abstract_idsconcatenated Paul Fisher 2010-03-10 18:39:09.356 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 2010-03-10 18:39:09.356 GMT Pathway to PubMed 2010-03-10 18:39:09.356 GMT