Get_homologous_from_NCBI_homoloGene_using_one_UniProt_accessionproteinAccession00 A UniProt protein Accession 2011-10-14 14:00:23.210 BST P99999 2011-10-14 14:00:27.114 BST taxonomyAcc00 9606 2011-10-14 14:04:10.351 BST Specie where to find homologous. Use a taxonomy accession. Input "all" if you would like to find homologous in all the species. 2011-10-14 14:04:03.823 BST homologousEBI_PICR__find_cross_references_for_protein_accessionsonlyActive0taxonId0searchDatabases1Protein_accessions0mapping_table00net.sf.taverna.t2.activitiesdataflow-activity1.3net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeonlyActive_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity false net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvoketaxonId_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesearchDatabases_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity REFSEQ net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSplit_string_into_string_list_by_regular_expression_2string0regex0split11net.sf.taverna.t2.activitieslocalworker-activity1.3net.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-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokenewLinenewline00net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity newline 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetProteinRefSeqAccstring0mappedProtein00net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity string 0 'text/plain' java.lang.String true mappedProtein 0 0 workflow org.embl.ebi.escience.scuflworkers.java.SplitByRegex UserNameHere 2011-10-14 14:40:26.434 BST net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokefilterOutBlankResultslist11list211net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity list1 1 text/plain java.lang.String true list2 1 1 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGet_homologous_from_NCBI_homoloGenespecie0proteinAccs0Beanshell_listOfResults22net.sf.taverna.t2.activitiesdataflow-activity1.3net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshelllist12list211net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity list1 2 text/plain java.lang.String true list2 1 1 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_2list12list211net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity list1 2 text/plain java.lang.String true list2 1 1 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeEBI_PICR__find_cross_references_for_protein_accessions_2searchDatabases1onlyActive0Protein_accessions0taxonId0mapping_table00net.sf.taverna.t2.activitiesdataflow-activity1.3net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSplit_string_into_string_list_by_regular_expressionregex0string0split11net.sf.taverna.t2.activitieslocalworker-activity1.3net.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-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregex_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity , net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokestring_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity SWISSPROT,TREMBL net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeonlyActive_value_1value00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity false net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSplit_string_into_string_list_by_regular_expression_2_2string0regex0split11net.sf.taverna.t2.activitieslocalworker-activity1.3net.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-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokenewLine_2newline00net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity newline 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeselectSecondColumnstring0mappedProtein00net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity string 0 'text/plain' java.lang.String true mappedProtein 0 0 workflow org.embl.ebi.escience.scuflworkers.java.SplitByRegex UserNameHere 2011-10-14 13:04:58.700 BST net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_2_2list12list211net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity list1 2 text/plain java.lang.String true list2 1 1 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeMerge_String_List_to_a_String_3stringlist1seperator0concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.3net.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-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeseperator_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity , net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeEBI_PICR__find_cross_references_for_protein_accessionsonlyActiveonlyActive_valuevalueEBI_PICR__find_cross_references_for_protein_accessionstaxonIdtaxonId_valuevalueEBI_PICR__find_cross_references_for_protein_accessionssearchDatabasessearchDatabases_valuevalueEBI_PICR__find_cross_references_for_protein_accessionsProtein_accessionsproteinAccessionSplit_string_into_string_list_by_regular_expression_2stringEBI_PICR__find_cross_references_for_protein_accessionsmapping_tableSplit_string_into_string_list_by_regular_expression_2regexnewLinenewlinegetProteinRefSeqAccstringSplit_string_into_string_list_by_regular_expression_2splitfilterOutBlankResultslist1getProteinRefSeqAccmappedProteinGet_homologous_from_NCBI_homoloGenespecietaxonomyAccGet_homologous_from_NCBI_homoloGeneproteinAccsfilterOutBlankResultslist2Beanshelllist1Get_homologous_from_NCBI_homoloGeneBeanshell_listOfResultsBeanshell_2list1Beanshelllist2EBI_PICR__find_cross_references_for_protein_accessions_2searchDatabasesSplit_string_into_string_list_by_regular_expressionsplitEBI_PICR__find_cross_references_for_protein_accessions_2onlyActiveonlyActive_value_1valueEBI_PICR__find_cross_references_for_protein_accessions_2Protein_accessionsBeanshell_2list2EBI_PICR__find_cross_references_for_protein_accessions_2taxonIdtaxonomyAccSplit_string_into_string_list_by_regular_expressionregexregex_valuevalueSplit_string_into_string_list_by_regular_expressionstringstring_valuevalueSplit_string_into_string_list_by_regular_expression_2_2stringEBI_PICR__find_cross_references_for_protein_accessions_2mapping_tableSplit_string_into_string_list_by_regular_expression_2_2regexnewLine_2newlineselectSecondColumnstringSplit_string_into_string_list_by_regular_expression_2_2splitBeanshell_2_2list1selectSecondColumnmappedProteinMerge_String_List_to_a_String_3stringlistBeanshell_2_2list2Merge_String_List_to_a_String_3seperatorseperator_valuevaluehomologousMerge_String_List_to_a_String_3concatenated 4fd8b9fc-d7a7-4ebd-91fe-f1a738c7efcc 2011-10-14 14:39:11.182 BST 4867750e-1131-48c4-939d-cc5c006614f3 2011-10-14 16:49:04.642 BST 80b5f958-7a32-49e3-9980-5ea85e7ff976 2011-10-14 15:26:26.809 BST Get homologous from NCBI homoloGene for one UniProt protein accession. Use PICR to convert UniProt to RefSeq, get homologous from homoloGene and convert RefSeq results to UniProt. Be patient, the workflows has to bring a file around 11Mb. ftp://ftp.ncbi.nlm.nih.gov/pub/HomoloGene/README 2011-10-14 17:24:25.31 BST 493eab4b-3a46-40c5-9e5e-d9d4203c2d67 2011-10-14 14:33:30.533 BST cf87c41f-dd01-417c-a08a-9cf46dc3c74a 2011-10-14 16:10:37.86 BST 78c7b00f-076e-4c88-9578-27eeb0a4f561 2011-10-14 16:20:47.293 BST e57f848e-817d-4157-8c64-3aca9d9f73ec 2011-10-14 14:48:15.73 BST Rafael C. Jimenez 2011-10-14 14:27:42.905 BST 43181f7c-e99f-465e-ad98-2008fdba556c 2011-10-14 17:24:35.204 BST eec627f7-d6ea-4763-85b8-14dce216bfc1 2011-10-14 14:28:39.827 BST b5531852-afa4-48f8-9746-01712c3c2e9f 2011-10-14 16:15:26.396 BST cca47e7f-6ad0-4deb-af3c-c36dcd27d4d5 2011-10-14 15:07:53.482 BST a901f614-2745-412b-8c34-2cffea964d1d 2011-10-14 14:40:44.743 BST Get homologous from NCBI homoloGene using one UniProt accession 2011-10-14 17:22:02.820 BST a6311218-6f7d-4263-b9f2-855d427e2f98 2011-10-14 15:27:50.387 BST cd47862c-9fee-42a0-bdc7-52d4d4434521 2011-10-14 14:06:04.514 BST 1a9eda0d-a327-4d8d-95c2-d28a64651e07 2011-10-14 16:39:43.205 BST 4d1abfa0-0973-490e-b353-69841637d508 2011-10-14 15:33:11.815 BST 4ff9f5d6-d1c9-4dfd-8661-488b01ab7e87 2011-10-14 15:01:04.85 BST 855d9a0a-3174-4217-9a2a-72fc5138285c 2011-10-14 17:20:31.989 BST 72f8cfd9-485d-407d-bbaa-2c6ba3694a41 2011-10-14 17:09:56.963 BST 54ba8db2-3d58-492c-9317-00a2112382e1 2011-10-14 16:04:12.922 BST 466bf68d-73e3-4ea2-a50a-c6d55546b81e 2011-10-14 14:35:17.922 BST 493eab4b-3a46-40c5-9e5e-d9d4203c2d67 2011-10-14 14:37:46.761 BST ff6a37f5-70e2-44ed-acda-b8ab331fb83d 2011-10-14 14:38:10.21 BST 1592daa0-7937-4373-8a90-cf287c0d8a77 2011-10-14 15:36:45.693 BST ec0ee587-bb5c-4c4d-9a6c-6252fbf4da9e 2011-10-14 15:31:19.707 BST 19201ff3-4330-4af0-9851-ec1203531542 2011-10-14 15:13:18.638 BST EBI_PICR__find_cross_references_for_protein_accessionsProtein_accessions00 Input a list (comma-separated values) of protein accessions 2011-05-29 13:03:08.70 BST ENSP00000307786,ENSP00000369497 2011-05-29 13:01:48.270 BST searchDatabases11 SWISSPROT 2011-05-18 08:48:33.320 BST Which databases do you want the cross-references for? You can add more than one. You can get a list of databases available in PICR using the method "getMappedDatabaseNames" from the same PICR service or looking at this document http://www.ebi.ac.uk/Tools/picr/WSDLDocumentation.do 2011-05-18 08:48:28.762 BST onlyActive00 Do you just want accession that are active (no-deprecated)? … write down "true" or "false". If you do not specify this parameter the workflow will not work. 2011-05-18 08:47:24.674 BST true 2011-05-18 08:47:28.100 BST taxonId00 Create a new value and leave it empty if you do not want to filter by specie. Chose a Taxa Id if you want to limit by specie … http://www.uniprot.org/taxonomy/?query=* 2011-05-18 08:47:05.919 BST 9606 2011-05-18 08:47:10.722 BST mapping_tablegetUPIForAccessionparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.3net.sf.taverna.t2.activities.wsdl.WSDLActivity http://www.ebi.ac.uk/Tools/picr/service?wsdl getUPIForAccession net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetUPIForAccession_inputsearchDatabases1onlyActive0taxonId0accession0output00net.sf.taverna.t2.activitieswsdl-activity1.3net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity accession 0 'text/plain' false ac_version 0 'text/plain' false searchDatabases 1 l('text/plain') false taxonId 0 'text/plain' false onlyActive 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="getUPIForAccession" name="parameters" qname="{http://www.ebi.ac.uk/picr/AccessionMappingService}getUPIForAccession"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="accession" qname="{http://www.ebi.ac.uk/picr/AccessionMappingService}&gt;getUPIForAccession&gt;accession" /><s:basetype optional="false" unbounded="false" typename="string" name="ac_version" qname="{http://www.ebi.ac.uk/picr/AccessionMappingService}&gt;getUPIForAccession&gt;ac_version" /><s:arraytype optional="false" unbounded="true" wrapped="false" typename="string" name="searchDatabases" qname="{http://www.ebi.ac.uk/picr/AccessionMappingService}&gt;getUPIForAccession&gt;searchDatabases"><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="false" unbounded="false" typename="string" name="taxonId" qname="{http://www.ebi.ac.uk/picr/AccessionMappingService}&gt;getUPIForAccession&gt;taxonId" /><s:basetype optional="false" unbounded="false" typename="boolean" name="onlyActive" qname="{http://www.ebi.ac.uk/picr/AccessionMappingService}&gt;getUPIForAccession&gt;onlyActive" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetUPIForAccession_outputinput0getUPIForAccessionReturn11net.sf.taverna.t2.activitieswsdl-activity1.3net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false getUPIForAccessionReturn 1 l('text/xml') 1 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getUPIForAccessionResponse" name="parameters" qname="{http://www.ebi.ac.uk/picr/AccessionMappingService}getUPIForAccessionResponse"><s:elements><s:arraytype optional="false" unbounded="true" wrapped="false" typename="UPEntry" name="getUPIForAccessionReturn" qname="{http://www.ebi.ac.uk/picr/AccessionMappingService}&gt;getUPIForAccessionResponse&gt;getUPIForAccessionReturn"><s:elementtype><s:complextype optional="false" unbounded="false" typename="UPEntry" name="" qname="{http://model.picr.ebi.ac.uk}UPEntry"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="CRC64" qname="{http://model.picr.ebi.ac.uk}UPEntry&gt;CRC64" /><s:basetype optional="false" unbounded="false" typename="string" name="UPI" qname="{http://model.picr.ebi.ac.uk}UPEntry&gt;UPI" /><s:arraytype optional="true" unbounded="true" wrapped="false" typename="CrossReference" name="identicalCrossReferences" qname="{http://model.picr.ebi.ac.uk}UPEntry&gt;identicalCrossReferences"><s:elementtype><s:complextype optional="false" unbounded="false" typename="CrossReference" name="" qname="{http://model.picr.ebi.ac.uk}CrossReference"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="accession" qname="{http://model.picr.ebi.ac.uk}CrossReference&gt;accession" /><s:basetype optional="false" unbounded="false" typename="string" name="accessionVersion" qname="{http://model.picr.ebi.ac.uk}CrossReference&gt;accessionVersion" /><s:basetype optional="false" unbounded="false" typename="string" name="databaseDescription" qname="{http://model.picr.ebi.ac.uk}CrossReference&gt;databaseDescription" /><s:basetype optional="false" unbounded="false" typename="string" name="databaseName" qname="{http://model.picr.ebi.ac.uk}CrossReference&gt;databaseName" /><s:basetype optional="false" unbounded="false" typename="dateTime" name="dateAdded" qname="{http://model.picr.ebi.ac.uk}CrossReference&gt;dateAdded" /><s:basetype optional="false" unbounded="false" typename="dateTime" name="dateDeleted" qname="{http://model.picr.ebi.ac.uk}CrossReference&gt;dateDeleted" /><s:basetype optional="false" unbounded="false" typename="boolean" name="deleted" qname="{http://model.picr.ebi.ac.uk}CrossReference&gt;deleted" /><s:basetype optional="false" unbounded="false" typename="string" name="gi" qname="{http://model.picr.ebi.ac.uk}CrossReference&gt;gi" /><s:basetype optional="false" unbounded="false" typename="string" name="taxonId" qname="{http://model.picr.ebi.ac.uk}CrossReference&gt;taxonId" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="true" wrapped="false" typename="CrossReference" name="logicalCrossReferences" qname="{http://model.picr.ebi.ac.uk}UPEntry&gt;logicalCrossReferences"><s:elementtype><s:complextype id="{http://model.picr.ebi.ac.uk}CrossReference" optional="false" unbounded="false" typename="CrossReference" name="" /></s:elementtype></s:arraytype><s:basetype optional="false" unbounded="false" typename="string" name="sequence" qname="{http://model.picr.ebi.ac.uk}UPEntry&gt;sequence" /><s:basetype optional="false" unbounded="false" typename="dateTime" name="timestamp" qname="{http://model.picr.ebi.ac.uk}UPEntry&gt;timestamp" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetUPIForAccession_getUPIForAccessionReturninput0identicalCrossReferences11net.sf.taverna.t2.activitieswsdl-activity1.3net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false CRC64 0 'text/plain' 0 UPI 0 'text/plain' 0 identicalCrossReferences 1 l('text/xml') 1 logicalCrossReferences 1 l('text/xml') 1 sequence 0 'text/plain' 0 timestamp 0 'text/plain' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="UPEntry" name="" qname="{http://model.picr.ebi.ac.uk}UPEntry"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="CRC64" qname="{http://model.picr.ebi.ac.uk}UPEntry&gt;CRC64" /><s:basetype optional="false" unbounded="false" typename="string" name="UPI" qname="{http://model.picr.ebi.ac.uk}UPEntry&gt;UPI" /><s:arraytype optional="true" unbounded="true" wrapped="false" typename="CrossReference" name="identicalCrossReferences" qname="{http://model.picr.ebi.ac.uk}UPEntry&gt;identicalCrossReferences"><s:elementtype><s:complextype optional="false" unbounded="false" typename="CrossReference" name="" qname="{http://model.picr.ebi.ac.uk}CrossReference"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="accession" qname="{http://model.picr.ebi.ac.uk}CrossReference&gt;accession" /><s:basetype optional="false" unbounded="false" typename="string" name="accessionVersion" qname="{http://model.picr.ebi.ac.uk}CrossReference&gt;accessionVersion" /><s:basetype optional="false" unbounded="false" typename="string" name="databaseDescription" qname="{http://model.picr.ebi.ac.uk}CrossReference&gt;databaseDescription" /><s:basetype optional="false" unbounded="false" typename="string" name="databaseName" qname="{http://model.picr.ebi.ac.uk}CrossReference&gt;databaseName" /><s:basetype optional="false" unbounded="false" typename="dateTime" name="dateAdded" qname="{http://model.picr.ebi.ac.uk}CrossReference&gt;dateAdded" /><s:basetype optional="false" unbounded="false" typename="dateTime" name="dateDeleted" qname="{http://model.picr.ebi.ac.uk}CrossReference&gt;dateDeleted" /><s:basetype optional="false" unbounded="false" typename="boolean" name="deleted" qname="{http://model.picr.ebi.ac.uk}CrossReference&gt;deleted" /><s:basetype optional="false" unbounded="false" typename="string" name="gi" qname="{http://model.picr.ebi.ac.uk}CrossReference&gt;gi" /><s:basetype optional="false" unbounded="false" typename="string" name="taxonId" qname="{http://model.picr.ebi.ac.uk}CrossReference&gt;taxonId" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="true" wrapped="false" typename="CrossReference" name="logicalCrossReferences" qname="{http://model.picr.ebi.ac.uk}UPEntry&gt;logicalCrossReferences"><s:elementtype><s:complextype id="{http://model.picr.ebi.ac.uk}CrossReference" optional="false" unbounded="false" typename="CrossReference" name="" /></s:elementtype></s:arraytype><s:basetype optional="false" unbounded="false" typename="string" name="sequence" qname="{http://model.picr.ebi.ac.uk}UPEntry&gt;sequence" /><s:basetype optional="false" unbounded="false" typename="dateTime" name="timestamp" qname="{http://model.picr.ebi.ac.uk}UPEntry&gt;timestamp" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetUPIForAccessionReturn_identicalCrossReferencesinput0accession00databaseName00taxonId00accessionVersion00net.sf.taverna.t2.activitieswsdl-activity1.3net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false accession 0 'text/plain' 0 accessionVersion 0 'text/plain' 0 databaseDescription 0 'text/plain' 0 databaseName 0 'text/plain' 0 dateAdded 0 'text/plain' 0 dateDeleted 0 'text/plain' 0 deleted 0 'text/plain' 0 gi 0 'text/plain' 0 taxonId 0 'text/plain' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="CrossReference" name="" qname="{http://model.picr.ebi.ac.uk}CrossReference"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="accession" qname="{http://model.picr.ebi.ac.uk}CrossReference&gt;accession" /><s:basetype optional="false" unbounded="false" typename="string" name="accessionVersion" qname="{http://model.picr.ebi.ac.uk}CrossReference&gt;accessionVersion" /><s:basetype optional="false" unbounded="false" typename="string" name="databaseDescription" qname="{http://model.picr.ebi.ac.uk}CrossReference&gt;databaseDescription" /><s:basetype optional="false" unbounded="false" typename="string" name="databaseName" qname="{http://model.picr.ebi.ac.uk}CrossReference&gt;databaseName" /><s:basetype optional="false" unbounded="false" typename="dateTime" name="dateAdded" qname="{http://model.picr.ebi.ac.uk}CrossReference&gt;dateAdded" /><s:basetype optional="false" unbounded="false" typename="dateTime" name="dateDeleted" qname="{http://model.picr.ebi.ac.uk}CrossReference&gt;dateDeleted" /><s:basetype optional="false" unbounded="false" typename="boolean" name="deleted" qname="{http://model.picr.ebi.ac.uk}CrossReference&gt;deleted" /><s:basetype optional="false" unbounded="false" typename="string" name="gi" qname="{http://model.picr.ebi.ac.uk}CrossReference&gt;gi" /><s:basetype optional="false" unbounded="false" typename="string" name="taxonId" qname="{http://model.picr.ebi.ac.uk}CrossReference&gt;taxonId" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokebuild_mapping_tablecrossReferenceAccs3databaseNames3accessionVersions3taxonIds3originalAccs1results00net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity originalAccs 1 text/plain java.lang.String true crossReferenceAccs 3 text/plain java.lang.String true databaseNames 3 text/plain java.lang.String true taxonIds 3 text/plain java.lang.String true accessionVersions 3 text/plain java.lang.String true results 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesplit_stringregex0string0split11net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity string 0 'text/plain' java.lang.String true regex 0 'text/plain' java.lang.String true split 1 1 workflow org.embl.ebi.escience.scuflworkers.java.SplitByRegex UserNameHere 2011-05-29 12:57:38.562 BST net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregex_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity , net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetUPIForAccessionparametersgetUPIForAccession_inputoutputgetUPIForAccession_inputsearchDatabasessearchDatabasesgetUPIForAccession_inputonlyActiveonlyActivegetUPIForAccession_inputtaxonIdtaxonIdgetUPIForAccession_inputaccessionsplit_stringsplitgetUPIForAccession_outputinputgetUPIForAccessionparametersgetUPIForAccession_getUPIForAccessionReturninputgetUPIForAccession_outputgetUPIForAccessionReturngetUPIForAccessionReturn_identicalCrossReferencesinputgetUPIForAccession_getUPIForAccessionReturnidenticalCrossReferencesbuild_mapping_tablecrossReferenceAccsgetUPIForAccessionReturn_identicalCrossReferencesaccessionbuild_mapping_tabledatabaseNamesgetUPIForAccessionReturn_identicalCrossReferencesdatabaseNamebuild_mapping_tableaccessionVersionsgetUPIForAccessionReturn_identicalCrossReferencesaccessionVersionbuild_mapping_tabletaxonIdsgetUPIForAccessionReturn_identicalCrossReferencestaxonIdbuild_mapping_tableoriginalAccssplit_stringsplitsplit_stringregexregex_valuevaluesplit_stringstringProtein_accessionsmapping_tablebuild_mapping_tableresults 761f8082-d028-496d-bb1c-d9690f8fb31c 2011-05-18 07:34:02.337 BST c7604164-c633-479c-af37-210ac6c8b3ea 2011-05-18 08:16:28.999 BST f49baecc-e9e5-4240-aca0-47c73016c58e 2011-05-18 07:48:20.20 BST EBI PICR, find cross-references for protein accessions 2011-05-18 08:15:33.230 BST 21af884e-458f-4234-ba8b-a462ffb45f0b 2011-05-18 09:17:43.558 BST 35ef885d-1373-4d40-8597-ba5b07cbda78 2011-05-18 08:52:43.442 BST 205fea89-5fc4-4541-8c11-781b0110fd5f 2011-05-18 07:37:33.205 BST 99f35bd2-b018-4695-b0a0-b83873ac4204 2011-05-18 07:50:43.983 BST Find cross-references (based on 100% sequence identity) for protein accessions from more than 95 distinct databases. For instance input a list of IPI accessions and find cross-references for Swissprot and Ensembl. Mappings can be limited by source database, taxonomic ID and activity status. 2011-05-18 08:13:45.883 BST f365598f-84e9-41c5-9dac-a3d75ee5a43b 2011-05-29 12:15:12.114 BST 41be1c5e-d834-45f7-9b3c-d464dae04c54 2011-05-29 12:59:44.276 BST 9696674a-29d4-4a7c-b9b7-f994380a5ada 2011-05-29 02:57:55.703 BST 8699f6be-f587-44d2-8c86-c0e74e5232c9 2011-05-18 08:49:52.753 BST e67869cb-4fa8-41c0-bfc9-f0d1b9b70818 2011-05-18 09:20:14.32 BST 3b3375da-905f-4f29-93b5-cd9241de9b3f 2011-05-18 07:52:21.846 BST da8428f6-e0ee-4b6c-90fd-1c1d9c2b994f 2011-05-29 13:05:38.686 BST a1fe0cfe-6945-4b8d-b392-0d93b75129b9 2011-05-18 08:24:35.315 BST 1da59d84-2695-447b-9191-d0d5098060e0 2011-05-29 12:58:30.517 BST 7aa06da4-2bc5-41b2-b05c-4320cbb21523 2011-05-18 09:00:46.670 BST 8ebb0413-76fc-4a12-b74a-dd70c4097f69 2011-05-18 09:16:13.262 BST e6dd081b-ea4b-468f-b11e-d38a97396793 2011-05-18 09:24:17.357 BST 2ce11204-18ee-4628-834a-b84fb8d3ce3c 2011-05-29 12:17:37.169 BST 755870c4-e673-4bc5-88d1-ce6b5354dbb5 2011-05-18 07:38:21.962 BST fb13dc79-dca6-4250-973d-3275d986381d 2011-05-29 03:00:42.756 BST b958fe71-cd1e-4dab-9442-ea1c0ce7bd0f 2011-05-29 02:59:01.82 BST Rafael C Jimenez 2011-05-18 08:46:20.213 BST a58a95fb-b6db-4d1c-811e-2ad5f3eb1aca 2011-05-18 09:15:08.902 BST 81d2c585-f3df-4f49-8609-42facc48b85d 2011-05-18 09:28:12.188 BST 699353f1-5474-42fb-92c1-f2a1488142bb 2011-05-29 13:03:21.697 BST Get_homologous_from_NCBI_homoloGeneproteinAccs00 A list of Refseq protein accessions to query. Use comma-separated values (CSV) 2011-10-13 18:23:03.930 BST XP_524741.2,NP_001003746.1 2011-10-13 18:23:13.163 BST specie00 9606 2011-10-13 18:19:44.460 BST Specie where to find homologous. Use a taxonomy accession. Input "all" if you would like to find homologous in all the species. 2011-10-13 18:20:13.274 BST Beanshell_listOfResultslistOfproteinAccsgetHomologousFrom_homoloGenespecie0queryAccs1homologeneUrlNCBI0listOfResults22net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity homologeneUrlNCBI 0 text/plain java.lang.String true queryAccs 1 text/plain java.lang.String true specie 0 text/plain java.lang.String true listOfResults 2 2 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokehomologeneUrlNCBI_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity ftp://ftp.ncbi.nlm.nih.gov/pub/HomoloGene/current/homologene.data net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSplit_string_into_string_list_by_regular_expressionregex0string0split11net.sf.taverna.t2.activitieslocalworker-activity1.3net.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-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregex_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity , net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetHomologousFrom_homoloGenespeciespeciegetHomologousFrom_homoloGenequeryAccsSplit_string_into_string_list_by_regular_expressionsplitgetHomologousFrom_homoloGenehomologeneUrlNCBIhomologeneUrlNCBI_valuevalueSplit_string_into_string_list_by_regular_expressionregexregex_valuevalueSplit_string_into_string_list_by_regular_expressionstringproteinAccsBeanshell_listOfResultsgetHomologousFrom_homoloGenelistOfResultslistOfproteinAccsSplit_string_into_string_list_by_regular_expressionsplit 274f5ad8-0715-44fb-bd70-ffc201a89dda 2011-10-13 18:25:28.514 BST Get homologous from NCBI homoloGene 2011-10-13 18:26:19.374 BST bf54b0e6-6dae-4702-a625-adf7b86cca3c 2011-10-13 18:29:00.341 BST fd5b4735-d40b-4f7a-9e96-16a86de35244 2011-10-13 18:13:22.714 BST b62064b9-4d4c-459b-bf16-dc62f06035a3 2011-10-13 18:33:47.37 BST Get homologous from NCBI homoloGene for a list of Refseq protein accessions. Be patient, the workflows has to bring a file around 11Mb. ftp://ftp.ncbi.nlm.nih.gov/pub/HomoloGene/README 2011-10-13 18:28:59.2 BST 7ccaa81c-cbce-42b8-a30e-84caf41c9a7c 2011-10-13 18:27:04.366 BST 831388bf-1e8c-4301-9903-ae37f1b6f72e 2011-10-13 18:30:45.976 BST Rafael C. Jimenez 2011-10-13 18:23:44.729 BST