Annotate_a_gene_listEntrez_gene_DB_ID00 The ID for the EntrezGene database (Erasmus MC ontology format). 2013-02-06 19:25:33.892 UTC EG 2013-02-06 11:12:23.506 UTC Entrez_gene_IDs11 1281 28959 7805 54829 6122 653881 401331 10156 7846 392437 2512 10457 8406 483 7139 64231 6696 6277 5641 3126 3123 302 303 305 11031 929 972 7431 3125 158471 6275 3122 9168 7076 653214 439953 5478 6281 4267 6284 1601 84790 1278 399942 10376 1192 710 4626 4621 4635 26509 4636 6678 10763 301 645715 1915 158078 441032 7351 3115 1462 3108 6303 642741 718 100133511 653879 1134 2202 1756 2014 1634 9332 4069 84617 51155 10577 7305 23643 4060 960 6387 3113 715 8635 1290 3428 414308 712 3150 5118 1277 716 4256 7412 1436 5997 70 4608 8673 3075 1293 10234 729659 6282 2013-02-06 11:32:07.703 UTC Genes to be annotated (Entrez gene format, see http://www.ncbi.nlm.nih.gov/gene) 2013-02-06 19:25:08.98 UTC Disease_or_syndrome_concept_set00 82 2013-02-06 11:12:27.823 UTC ID of the predefined concept set to match with. These IDs can be retrieved by running the List Concept Sets workflow (http://www.myexperiment.org/workflows/2999). The example ID corresponds to the concept set "Disease or Syndrome". 2013-02-06 19:26:22.730 UTC Match_concept_cutoff00 5 2013-02-06 13:45:42.907 UTC Max number of concepts to return from the concept profile matching procedure. 2013-02-06 19:24:05.487 UTC Explained_concepts_cutoff00 Max number of explanatory concepts to return for a concept profile match. 2013-02-06 19:40:41.833 UTC 10 2013-02-06 13:59:45.824 UTC Matched_disease_names muscular dystrophy, duchenne hereditary angioneurotic edema osteogenesis imperfecta LGMD2B Rieger syndrome 2013-02-06 19:48:47.811 UTC Names for the concepts from the concept profile match. 2013-02-06 19:48:22.482 UTC Summed_Similarity_score Concept match similarity score from the matching procedure. 2013-02-06 19:46:50.179 UTC 0.00885673714427425 0.007450532171402273 0.00504372819304191 0.004096281111489342 0.0038713032622080803 2013-02-06 19:47:05.505 UTC Explained_concept_name Example list to large to list here, below a subset. muscular dystrophy 2013-02-06 19:52:05.875 UTC The concept names of the explanatory concepts. 2013-02-06 19:51:33.921 UTC Explained_concept_ID Example list to large to list here, below a subset. http://rdf.biosemantics.org/owl/concept#26850 2013-02-06 19:52:25.262 UTC The concept IDs of the explanatory concepts. 2013-02-06 19:52:37.886 UTC Match_concept_ID IDs for the concepts from the concept profile match. 2013-02-06 19:49:05.859 UTC http://rdf.biosemantics.org/owl/concept#13264 http://rdf.biosemantics.org/owl/concept#19243 http://rdf.biosemantics.org/owl/concept#29434 http://rdf.biosemantics.org/owl/concept#1850889 http://rdf.biosemantics.org/owl/concept#265341 2013-02-06 19:49:21.658 UTC Query_concept_ID Example list to large to list here, below a subset. http://rdf.biosemantics.org/owl/concept#3091526 2013-02-06 19:51:07.660 UTC IDs for the concepts from the concept profile query. 2013-02-06 19:49:43.174 UTC Match_concept_profilesCutoff0Match_concept_set0Query_concept_ID0Similarity_score11Match_concept_ID11Query_concept_ID11 Purpose of component in workflow: The purpose of this component (nested workflow) in this workflow is to match the concept profiles of genes to the profiles of disease concepts (from the Disease or Syndrome branch). Results: The results of this component are diseases associated with genes, ranked in the order of the match score between the input concepts. The results suggest which diseases are associated with the difference in gene expression in the underlying experiment. 2013-02-06 19:37:58.222 UTC net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeDatabaseID_to_ConceptIDDatabaseID0IDvalue0Concept_IDs00 Purpose of component in workflow: The purpose of this component (nested workflow) here is to map Entrez gene identifiers (the external database identifiers) to the concept identifier used in the Erasmus MC ontology, developed by the BioSemantics Group in Rotterdam. The ontology can be seen as a concept database compiled from various common thesauri and ontologies. 2013-02-06 19:32:51.153 UTC net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSplit_string_into_string_list_by_regular_expressionregex0string0split11 This local service prepares the list of genes for fast processing: make comma-separated list. 2013-02-06 19:43:15.296 UTC net.sf.taverna.t2.activitieslocalworker-activity1.4net.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-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeText_constantvalue00 The constant that is used by the local service, in this case ",". 2013-02-06 19:44:09.439 UTC net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity \n net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGet_concept_nameConcept_ID0Concept_name00 Purpose of component in workflow: To retrieve the name of the concept from the ontology. 2013-02-06 19:38:43.270 UTC net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeMerge_String_List_to_a_Stringseperator0stringlist1concatenated00 This local service prepares the list of concepts for fast processing: make comma-separated list. 2013-02-06 19:43:30.163 UTC net.sf.taverna.t2.activitieslocalworker-activity1.4net.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-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeText_constant_2value00 The constant that is used by the local service, in this case ",". 2013-02-06 19:44:22.819 UTC net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity , net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExplain_concept_scoresC_ConceptID0cutoff0A_ConceptID0B_ConceptName11B_ConceptID11 Purpose of component in workflow: This component retieves the concepts contributing most to the match perfomed in the Match_concept_profiles component. 2013-02-06 19:38:26.626 UTC net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeMatch_concept_profilesCutoffMatch_concept_cutoffMatch_concept_profilesMatch_concept_setDisease_or_syndrome_concept_setMatch_concept_profilesQuery_concept_IDMerge_String_List_to_a_StringconcatenatedDatabaseID_to_ConceptIDDatabaseIDEntrez_gene_DB_IDDatabaseID_to_ConceptIDIDvalueSplit_string_into_string_list_by_regular_expressionsplitSplit_string_into_string_list_by_regular_expressionregexText_constantvalueSplit_string_into_string_list_by_regular_expressionstringEntrez_gene_IDsGet_concept_nameConcept_IDMatch_concept_profilesMatch_concept_IDMerge_String_List_to_a_StringseperatorText_constant_2valueMerge_String_List_to_a_StringstringlistDatabaseID_to_ConceptIDConcept_IDsExplain_concept_scoresC_ConceptIDMatch_concept_profilesQuery_concept_IDExplain_concept_scorescutoffExplained_concepts_cutoffExplain_concept_scoresA_ConceptIDMatch_concept_profilesMatch_concept_IDMatched_disease_namesGet_concept_nameConcept_nameSummed_Similarity_scoreMatch_concept_profilesSimilarity_scoreExplained_concept_nameExplain_concept_scoresB_ConceptNameExplained_concept_IDExplain_concept_scoresB_ConceptIDMatch_concept_IDMatch_concept_profilesMatch_concept_IDQuery_concept_IDMatch_concept_profilesQuery_concept_ID 7df07095-ba57-402a-bc57-b062f18c0382 2013-02-06 11:33:13.41 UTC 9ef22893-9445-4ae4-bf1d-de9ad42d7e50 2013-02-06 11:17:08.710 UTC b7517a66-bb6a-4969-862d-34921f5f620a 2013-02-06 19:57:24.333 UTC 13f5ae83-f313-438b-8ca7-5bf638b9579f 2013-02-06 13:45:44.424 UTC 8333ebc4-ec35-4bba-bbb3-2d89f78bb432 2013-02-06 13:08:17.940 UTC Purpose: Currently, this workflow takes a list of genes and a concept set as input, calculates the matching score between these and finds the concept that contributes the most to the match. Author comments: The workflow is in Beta stage. It runs, but needs more testing with different parameter settings. This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/368 for functional gene annotation and knowledge discovery. 2013-02-06 19:57:24.182 UTC f41926bc-1173-4cd6-94ce-34f8bb10e115 2013-02-06 14:17:28.659 UTC 05e6f84d-b606-4ee1-8dbd-b3fc813a0587 2013-02-06 18:55:44.517 UTC a950ef98-59af-499c-9fcc-bfe9101ff90d 2013-02-06 18:58:12.960 UTC b1337230-2045-44a4-a98e-2710e8286c31 2013-02-06 11:36:47.649 UTC Authors: Kristina Hettne Contributors: Reinout van Schouwen, Marco Roos 2013-02-06 19:54:27.608 UTC 0f2d6ede-2dba-45ac-ae26-d5164adc885b 2013-02-06 11:13:59.426 UTC 73bd51a5-526f-4079-a740-b34a1abfe2dd 2013-02-06 13:12:36.724 UTC 725ac5d6-1a69-4240-9461-f2b5e9bbdf6a 2013-02-06 14:02:17.849 UTC 37cdecaa-ca6d-4e38-b096-da19215ff26c 2013-02-06 11:46:37.385 UTC 8e439818-7a37-42e0-90db-7c800600f736 2013-02-06 12:49:41.433 UTC c9e941cd-6f71-440b-afd2-04ec26929acc 2013-02-06 13:21:01.258 UTC 9eedfbed-82d1-4ba5-9c5b-8c92c2c740b9 2013-02-06 14:00:13.266 UTC 8dab1252-b6f6-4c00-8e71-6fb74d9f5253 2013-02-06 19:44:22.964 UTC fe01d839-8fb8-4243-8b0c-0c03856eab61 2013-02-06 14:29:55.480 UTC ee47e8f0-8809-4408-85df-6369a8448494 2013-02-06 19:52:38.18 UTC Annotate a gene list with disease concepts 2013-02-06 19:54:56.223 UTC aedced2a-49f2-449b-8a73-e85e495ec0c2 2013-02-06 11:49:19.279 UTC d2b86eb3-5a8a-4225-9b49-11827828fe40 2013-02-06 12:41:31.510 UTC daa2955a-ae29-48d4-845a-4ae77500e748 2013-02-06 19:39:14.176 UTC DatabaseID_to_ConceptIDDatabaseID00 Identifier for databases, e.g. EG for Entrez Gene Possible values: EG, Entrez Gene 2012-06-25 20:38:10.999 UTC EG 2012-04-24 23:16:44.86 UTC IDvalue00 3064 2012-04-24 23:17:45.507 UTC Identifier value, e.g. 3064 for HTT when DatabaseID=EG 2012-06-25 20:37:53.622 UTC Concept_IDs http://rdf.biosemantics.org/owl/concept#33097212 2013-02-05 21:21:56.659 UTC Concept Identifiers for the given input, e.g. 3097212 for EG.3064 2012-04-24 23:19:16.717 UTC mapDatabaseIDToConceptIDsparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivity http://ws.biosemantics.org/ConceptRecognizerService?wsdl mapDatabaseIDToConceptIDs net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 3 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemapDatabaseIDToConceptIDs_inputID0database0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity database 0 'text/plain' false ID 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="mapDatabaseIDToConceptIDs" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}mapDatabaseIDToConceptIDs"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="database" qname="mapDatabaseIDToConceptIDs&gt;database" /><s:basetype optional="true" unbounded="false" typename="string" name="ID" qname="mapDatabaseIDToConceptIDs&gt;ID" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemapDatabaseIDToConceptIDs_outputinput0return00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false return 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="mapDatabaseIDToConceptIDsResponse" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}mapDatabaseIDToConceptIDsResponse"><s:elements><s:complextype optional="true" unbounded="false" typename="conceptSetWrapper" name="return" qname="mapDatabaseIDToConceptIDsResponse&gt;return"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptIDsAsString" qname="conceptSetWrapper&gt;conceptIDsAsString" /></s:elements></s:complextype></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemapDatabaseIDToConceptIDs_returninput0conceptIDsAsString00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false conceptIDsAsString 0 'text/plain' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="true" unbounded="false" typename="conceptSetWrapper" name="return" qname="mapDatabaseIDToConceptIDsResponse&gt;return"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptIDsAsString" qname="conceptSetWrapper&gt;conceptIDsAsString" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemapDatabaseIDToConceptIDsparametersmapDatabaseIDToConceptIDs_inputoutputmapDatabaseIDToConceptIDs_inputIDIDvaluemapDatabaseIDToConceptIDs_inputdatabaseDatabaseIDmapDatabaseIDToConceptIDs_outputinputmapDatabaseIDToConceptIDsparametersmapDatabaseIDToConceptIDs_returninputmapDatabaseIDToConceptIDs_outputreturnConcept_IDsmapDatabaseIDToConceptIDs_returnconceptIDsAsString 7c52983e-1954-409c-bbc6-2f026465c523 2013-02-06 12:47:08.143 UTC c2cbb1b4-e2b2-4c45-9dfd-5323f702be83 2012-04-24 23:22:49.83 UTC 0b447fad-9299-453c-9195-e00c9fb687a7 2012-04-24 23:20:02.840 UTC 80ee33e8-dddc-4d0f-aef9-ce9790e69904 2012-04-24 23:12:44.984 UTC 7ecf19fa-7ed5-489c-82e5-9b2468795c30 2012-09-04 11:14:44.543 UTC 60ef0156-46c6-4368-a578-e6a26823caba 2013-01-28 15:03:01.417 UTC c690ec55-e66d-4cde-a257-f219ab141679 2013-02-05 11:51:05.313 UTC d2f0a621-0e45-43b7-bd56-11c61a1c8df9 2012-07-18 13:13:11.179 UTC Purpose: This workflow maps input Identifiers, common database identifiers, to the Concept Identifiers from the EMC ontology. Result: Concept Identifiers from the EMC ontology. Resources: Table of database identifiers and concept identifiers. Database identifiers from ... EMC ontology compiled from ... Comments: This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery. 2012-07-18 13:12:53.96 UTC 37daa1ca-9ddd-49a3-a622-41481f0a3c35 2013-02-05 21:21:58.367 UTC cdf66f51-8d56-4a5f-87c7-5b8dbd434ee8 2012-07-11 14:23:57.252 UTC Authors: Marco Roos on behalf of the BioSemantics group Contributors: Web Service by Reinout van Schouwen Additional annotations by Kristina Hettne 2012-07-18 13:12:00.232 UTC DatabaseID_to_ConceptID 2012-04-24 23:22:45.412 UTC 14fee9a1-cd21-44f2-9f28-4f2362b8d667 2012-06-25 20:39:09.656 UTC d5450be7-b43d-4037-9a2c-8fe0d8019513 2013-02-06 12:37:40.862 UTC Explain_concept_scoresC_ConceptID00 The concept id of the C concept. 2012-09-11 09:01:25.824 UTC http://rdf.biosemantics.org/owl/concept#2263126 2013-02-05 20:09:11.301 UTC cutoff00 1 2012-09-10 15:18:30.889 UTC Maximum number of explanatory concepts to return. 2012-09-11 08:30:14.173 UTC A_ConceptID00 http://rdf.biosemantics.org/owl/concept#3096431 2013-02-05 20:09:19.271 UTC The concept id of the A concept. 2012-09-11 09:01:33.736 UTC B_ConceptName The concept name of the explanatory B concept. 2012-09-11 09:01:44.136 UTC FADS2 2012-09-10 15:17:05.627 UTC B_ConceptID The concept ID of the explanatory B concept. 2012-09-11 09:01:40.385 UTC http://rdf.biosemantics.org/owl/concept#3096431 2013-02-05 20:09:37.980 UTC B_ConceptContribution The contribution score, that is, the percentage of the contributions of the individual concepts to the coherence score (the average of the inner product scores of all possible concept pairs within the group). 2012-09-11 08:58:01.819 UTC 43.36232841014862 2012-09-10 15:16:19.600 UTC explainScoresStringInputparameters0parameters00 This Web service takes two concept ids as input and returns the top ranking "B" concepts according to Swanson's ABC model of discovery, where the relationships AB and BC are known and reported in the literature, and the implicit relationship AC is a putative new discovery. It might also be the case that AC is already known. In that case AC does not represent a new discovery but will still be returned by the Web service. The concept contribution is also reported by the Web service. The concept contribution is the percentage of the contributions of the individual concepts to the coherence score (the average of the inner product scores of all possible concept pairs within the group). 2012-09-11 08:57:10.939 UTC net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivity http://ws.biosemantics.org/ConceptRecognizerService?wsdl explainScoresStringInput net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeexplainScoresStringInput_inputcutoffValue0conceptCUIsAsString0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity cutoffValue 0 'text/plain' false conceptCUIsAsString 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="explainScoresStringInput" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}explainScoresStringInput"><s:elements><s:basetype optional="false" unbounded="false" typename="int" name="cutoffValue" qname="explainScoresStringInput&gt;cutoffValue" /><s:basetype optional="true" unbounded="false" typename="string" name="conceptCUIsAsString" qname="explainScoresStringInput&gt;conceptCUIsAsString" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeexplainScoresStringInput_outputinput0return00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false return 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="explainScoresStringInputResponse" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}explainScoresStringInputResponse"><s:elements><s:complextype optional="true" unbounded="false" typename="conceptContributionsWrapper" name="return" qname="explainScoresStringInputResponse&gt;return"><s:elements><s:arraytype optional="true" unbounded="false" wrapped="true" typename="&gt;conceptContributionsWrapper&gt;ConceptContributionTable" name="ConceptContributionTable" qname="conceptContributionsWrapper&gt;ConceptContributionTable"><s:elementtype><s:complextype optional="false" unbounded="false" typename="conceptContribution" name="" qname="{http://services.conceptrecognizer.lumc.nl/}conceptContribution"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptName" qname="conceptContribution&gt;conceptName" /><s:basetype optional="true" unbounded="false" typename="double" name="contribution" qname="conceptContribution&gt;contribution" /><s:basetype optional="true" unbounded="false" typename="int" name="conceptId" qname="conceptContribution&gt;conceptId" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeexplainScoresStringInput_returninput0ConceptContributionTable00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false ConceptContributionTable 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="true" unbounded="false" typename="conceptContributionsWrapper" name="return" qname="explainScoresStringInputResponse&gt;return"><s:elements><s:arraytype optional="true" unbounded="false" wrapped="true" typename="&gt;conceptContributionsWrapper&gt;ConceptContributionTable" name="ConceptContributionTable" qname="conceptContributionsWrapper&gt;ConceptContributionTable"><s:elementtype><s:complextype optional="false" unbounded="false" typename="conceptContribution" name="" qname="{http://services.conceptrecognizer.lumc.nl/}conceptContribution"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptName" qname="conceptContribution&gt;conceptName" /><s:basetype optional="true" unbounded="false" typename="double" name="contribution" qname="conceptContribution&gt;contribution" /><s:basetype optional="true" unbounded="false" typename="int" name="conceptId" qname="conceptContribution&gt;conceptId" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokereturn_ConceptContributionTable_2input0ConceptContributionTable11net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false ConceptContributionTable 1 l('text/xml') 1 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:arraytype optional="true" unbounded="false" wrapped="true" typename="&gt;conceptContributionsWrapper&gt;ConceptContributionTable" name="ConceptContributionTable" qname="conceptContributionsWrapper&gt;ConceptContributionTable"><s:elementtype><s:complextype optional="false" unbounded="false" typename="conceptContribution" name="" qname="{http://services.conceptrecognizer.lumc.nl/}conceptContribution"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptName" qname="conceptContribution&gt;conceptName" /><s:basetype optional="true" unbounded="false" typename="double" name="contribution" qname="conceptContribution&gt;contribution" /><s:basetype optional="true" unbounded="false" typename="int" name="conceptId" qname="conceptContribution&gt;conceptId" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke2_ConceptContributionTableinput0contribution00conceptId00conceptName00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false conceptName 0 'text/plain' 0 contribution 0 'text/plain' 0 conceptId 0 'text/plain' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="conceptContribution" name="" qname="{http://services.conceptrecognizer.lumc.nl/}conceptContribution"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptName" qname="conceptContribution&gt;conceptName" /><s:basetype optional="true" unbounded="false" typename="double" name="contribution" qname="conceptContribution&gt;contribution" /><s:basetype optional="true" unbounded="false" typename="int" name="conceptId" qname="conceptContribution&gt;conceptId" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemakeCommaSeparatedStringitem20item10output00 This script concatenates the two input concept id strings and adds a comma in between. 2012-09-11 08:29:47.911 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity item1 0 text/plain java.lang.String true item2 0 text/plain java.lang.String true output 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeexplainScoresStringInputparametersexplainScoresStringInput_inputoutputexplainScoresStringInput_inputcutoffValuecutoffexplainScoresStringInput_inputconceptCUIsAsStringmakeCommaSeparatedStringoutputexplainScoresStringInput_outputinputexplainScoresStringInputparametersexplainScoresStringInput_returninputexplainScoresStringInput_outputreturnreturn_ConceptContributionTable_2inputexplainScoresStringInput_returnConceptContributionTable2_ConceptContributionTableinputreturn_ConceptContributionTable_2ConceptContributionTablemakeCommaSeparatedStringitem2C_ConceptIDmakeCommaSeparatedStringitem1A_ConceptIDB_ConceptName2_ConceptContributionTableconceptNameB_ConceptID2_ConceptContributionTableconceptIdB_ConceptContribution2_ConceptContributionTablecontribution abaeb048-e186-4c8d-92d4-6b32b22603d8 2012-04-16 13:01:16.427 UTC bb8d1d77-e3d2-4cee-aee9-3cd4e1bd8547 2012-01-06 12:38:00.681 UTC 7a995f89-0c37-48b9-b0f7-8eca5cd36420 2012-01-06 11:51:06.790 UTC 0faa8a91-3a1c-4e03-b74d-f271e7b96290 2012-04-16 12:55:56.499 UTC a6c096b8-050d-48bf-8b9c-114762aac26d 2012-09-07 14:52:03.90 UTC 2b762f5e-4473-4d48-b78f-df306600467a 2012-09-11 09:11:13.838 UTC 13050a9d-bdda-4de5-8bc7-8503457302cd 2012-04-16 13:02:36.340 UTC 6bab82da-54d0-4bc7-96fd-e5c5d3c6d77f 2012-09-07 14:37:53.808 UTC 541a7a2d-e3e3-490d-885b-52d653a21d11 2012-02-03 11:42:15.89 UTC 9e4c2fcc-6dcc-46d5-9edd-d7841389ef5c 2012-04-17 08:22:27.551 UTC 4f826cfe-3950-4151-bbe6-bff67413be51 2012-09-07 15:22:15.103 UTC Purpose of workflow: This workflow takes two concept ids as input and returns the top ranking "B" concepts according to Swanson's ABC model of discovery, where the relationships AB and BC are known and reported in the literature, and the implicit relationship AC is a putative new discovery. It might also be the case that AC is already known. In that case AC does not represent a new discovery but will still be returned (see workflow example values). The B concepts are returned sorted on the percentage of the contributions of the individual concepts to the coherence score (the average of the inner product scores of all possible concept pairs within the group). This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery. 2012-09-11 09:11:13.758 UTC 7d6ba6db-2552-4c15-b800-1789f5385d44 2012-09-07 15:18:14.352 UTC 1ea652c5-572b-4b0a-b66d-5ae41a7b7fe1 2013-02-05 09:41:27.678 UTC 8f284446-2578-4c4d-b81d-e842a463641b 2012-09-07 15:34:00.455 UTC 90f0af1e-a653-4a85-889c-4120accdd9d9 2012-09-07 14:44:36.440 UTC 8efd062c-22d8-4fc6-bfe4-ea8f96ba7e2a 2012-04-16 12:58:21.8 UTC 09802e77-93ac-45ba-9ad5-e7bea33cda8b 2013-02-05 20:09:38.174 UTC 8d4a9091-0ba9-468e-9883-7b08e5212cd2 2012-04-16 13:07:32.864 UTC 713fa342-cdf4-48b7-850d-abecb37b9b1f 2012-09-11 08:58:13.328 UTC c416805f-aa9d-4d44-b434-f253935ed0ef 2012-09-11 08:57:11.33 UTC Explain concept scores 2012-04-16 13:00:42.27 UTC a260c127-7bbc-4dde-86a9-80647fcbb862 2012-09-10 15:18:42.957 UTC 88e1d0d3-3377-4a21-a98f-19020444e686 2012-09-07 14:58:20.922 UTC 89f2da6a-161b-47b1-a048-a65fd35f912c 2012-01-06 11:47:16.46 UTC 4b937a61-6180-48ce-a679-cf3ed1c8f208 2012-09-11 08:58:54.136 UTC fc7ae322-fcac-41c5-b136-0767d52680b0 2012-03-21 13:53:26.66 UTC 142a2c6d-8e96-4c9f-ad64-da97fd4c2597 2012-09-04 11:16:44.759 UTC 3c6eca00-e3a8-46b8-86bd-7c4b48a3ac77 2012-07-18 13:20:01.872 UTC 9a6508bd-87c3-4d9c-99f2-9003b5b57df4 2012-09-11 09:01:50.31 UTC 4bed166d-9815-4a35-a613-869b300b7973 2012-04-16 13:04:34.678 UTC 2b5167d3-3864-46c1-b761-b66ab721da54 2012-02-03 13:52:44.748 UTC Creator: Reinout van Schouwen on behalf of the BIoSemantics Group Adaptations by Marco Roos and Kristina Hettne 2012-09-11 09:02:52.112 UTC Match_concept_profilCutoff00 The number of resulting matched concepts that will be shown. 2012-04-16 12:36:29.53 UTC 1 2013-02-05 19:53:47.84 UTC Match_concept_set00 The ConceptSet that is to be matched. A list of IDs for the predifined concept sets can be retrieved by running the List Concept Sets workflow (http://www.myexperiment.org/workflows/2999). The example ID corresponds to the concept set GO Biological Processes. 2013-02-05 20:18:48.820 UTC 5 2013-01-07 13:18:28.976 UTC Query_concept_ID00 http://rdf.biosemantics.org/owl/concept#4275360 2013-02-05 20:12:35.528 UTC The ConceptSet (a list of concept identifiers) to be queried. For example: 4275360 2012-04-16 12:39:57.499 UTC Match_concept_ID <http://rdf.biosemantics.org/owl/concept#1156814/> 2013-01-29 14:24:54.220 UTC Concept ID of the matched concept. 2013-01-29 14:25:01.866 UTC Similarity_score 0.0016150908923791584 2013-01-29 14:25:31.229 UTC List of similarity scores for the matched concept profiles. 2012-09-11 12:29:44.886 UTC Query_concept_IDgetSimilarConceptProfilesPredefinedparameters0parameters00 The Web service takes a (list of) concept identifiers and the ID for the predefined concept set as input and calculates the matching score between the concept profiles of the concepts according to the scaled inner product. A list of IDs for the predifined concept sets can be retrieved by running the List Concept Sets workflow (http://www.myexperiment.org/workflows/2999). The example ID corresponds to the concept set GO Biological Processes. 2013-02-05 20:18:25.345 UTC net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivity http://ws.biosemantics.org/ConceptRecognizerService?wsdl getSimilarConceptProfilesPredefined net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetSimilarConceptProfilesPredefined_inputcutoffValue0conceptSetId0queryConceptProfileList0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity cutoffValue 0 'text/plain' false conceptSetId 0 'text/plain' false queryConceptProfileList 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="getSimilarConceptProfilesPredefined" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}getSimilarConceptProfilesPredefined"><s:elements><s:basetype optional="false" unbounded="false" typename="int" name="cutoffValue" qname="getSimilarConceptProfilesPredefined&gt;cutoffValue" /><s:basetype optional="false" unbounded="false" typename="int" name="conceptSetId" qname="getSimilarConceptProfilesPredefined&gt;conceptSetId" /><s:basetype optional="true" unbounded="false" typename="string" name="queryConceptProfileList" qname="getSimilarConceptProfilesPredefined&gt;queryConceptProfileList" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetSimilarConceptProfilesPredefined_outputinput0return00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false return 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getSimilarConceptProfilesPredefinedResponse" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}getSimilarConceptProfilesPredefinedResponse"><s:elements><s:complextype optional="true" unbounded="false" typename="matchingResult" name="return" qname="getSimilarConceptProfilesPredefinedResponse&gt;return"><s:elements><s:arraytype optional="true" unbounded="false" wrapped="true" typename="&gt;matchingResult&gt;MatchConceptProfileList" name="MatchConceptProfileList" qname="matchingResult&gt;MatchConceptProfileList"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="similarityScoreLists" name="SimilarityScoreLists" qname="matchingResult&gt;SimilarityScoreLists"><s:elementtype><s:complextype optional="false" unbounded="false" typename="scoreListImpl" name="" qname="{http://services.conceptrecognizer.lumc.nl/}scoreListImpl"><s:elements><s:arraytype optional="true" unbounded="true" wrapped="false" typename="stringDoubleTuple" name="QueryScoreTupleList" qname="scoreListImpl&gt;QueryScoreTupleList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="stringDoubleTuple" name="" qname="{http://services.conceptrecognizer.lumc.nl/}stringDoubleTuple"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="queryConceptID" qname="stringDoubleTuple&gt;queryConceptID" /><s:basetype optional="true" unbounded="false" typename="double" name="score" qname="stringDoubleTuple&gt;score" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:basetype optional="true" unbounded="false" typename="string" name="conceptId" qname="scoreListImpl&gt;conceptId" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="&gt;matchingResult&gt;SummedSimilarityScoreList" name="SummedSimilarityScoreList" qname="matchingResult&gt;SummedSimilarityScoreList"><s:elementtype><s:basetype optional="false" unbounded="false" typename="double" name="" qname="{http://www.w3.org/2001/XMLSchema}double" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetSimilarConceptProfilesPredefined_returninput0SummedSimilarityScoreList11MatchConceptProfileList11SimilarityScoreLists00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false MatchConceptProfileList 1 l('text/plain') 1 SimilarityScoreLists 0 'text/xml' 0 SummedSimilarityScoreList 1 l('text/plain') 1 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="true" unbounded="false" typename="matchingResult" name="return" qname="getSimilarConceptProfilesPredefinedResponse&gt;return"><s:elements><s:arraytype optional="true" unbounded="false" wrapped="true" typename="&gt;matchingResult&gt;MatchConceptProfileList" name="MatchConceptProfileList" qname="matchingResult&gt;MatchConceptProfileList"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="similarityScoreLists" name="SimilarityScoreLists" qname="matchingResult&gt;SimilarityScoreLists"><s:elementtype><s:complextype optional="false" unbounded="false" typename="scoreListImpl" name="" qname="{http://services.conceptrecognizer.lumc.nl/}scoreListImpl"><s:elements><s:arraytype optional="true" unbounded="true" wrapped="false" typename="stringDoubleTuple" name="QueryScoreTupleList" qname="scoreListImpl&gt;QueryScoreTupleList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="stringDoubleTuple" name="" qname="{http://services.conceptrecognizer.lumc.nl/}stringDoubleTuple"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="queryConceptID" qname="stringDoubleTuple&gt;queryConceptID" /><s:basetype optional="true" unbounded="false" typename="double" name="score" qname="stringDoubleTuple&gt;score" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:basetype optional="true" unbounded="false" typename="string" name="conceptId" qname="scoreListImpl&gt;conceptId" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="&gt;matchingResult&gt;SummedSimilarityScoreList" name="SummedSimilarityScoreList" qname="matchingResult&gt;SummedSimilarityScoreList"><s:elementtype><s:basetype optional="false" unbounded="false" typename="double" name="" qname="{http://www.w3.org/2001/XMLSchema}double" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokereturn_SimilarityScoreListsinput0SimilarityScoreLists11net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false SimilarityScoreLists 1 l('text/xml') 1 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:arraytype optional="true" unbounded="false" wrapped="true" typename="similarityScoreLists" name="SimilarityScoreLists" qname="matchingResult&gt;SimilarityScoreLists"><s:elementtype><s:complextype optional="false" unbounded="false" typename="scoreListImpl" name="" qname="{http://services.conceptrecognizer.lumc.nl/}scoreListImpl"><s:elements><s:arraytype optional="true" unbounded="true" wrapped="false" typename="stringDoubleTuple" name="QueryScoreTupleList" qname="scoreListImpl&gt;QueryScoreTupleList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="stringDoubleTuple" name="" qname="{http://services.conceptrecognizer.lumc.nl/}stringDoubleTuple"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="queryConceptID" qname="stringDoubleTuple&gt;queryConceptID" /><s:basetype optional="true" unbounded="false" typename="double" name="score" qname="stringDoubleTuple&gt;score" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:basetype optional="true" unbounded="false" typename="string" name="conceptId" qname="scoreListImpl&gt;conceptId" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSimilarityScoreLists_SimilarityScoreListsinput0QueryScoreTupleList11net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false QueryScoreTupleList 1 l('text/xml') 1 conceptId 0 'text/plain' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="scoreListImpl" name="" qname="{http://services.conceptrecognizer.lumc.nl/}scoreListImpl"><s:elements><s:arraytype optional="true" unbounded="true" wrapped="false" typename="stringDoubleTuple" name="QueryScoreTupleList" qname="scoreListImpl&gt;QueryScoreTupleList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="stringDoubleTuple" name="" qname="{http://services.conceptrecognizer.lumc.nl/}stringDoubleTuple"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="queryConceptID" qname="stringDoubleTuple&gt;queryConceptID" /><s:basetype optional="true" unbounded="false" typename="double" name="score" qname="stringDoubleTuple&gt;score" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:basetype optional="true" unbounded="false" typename="string" name="conceptId" qname="scoreListImpl&gt;conceptId" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSimilarityScoreLists_QueryScoreTupleListinput0queryConceptID00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false queryConceptID 0 'text/plain' 0 score 0 'text/plain' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="stringDoubleTuple" name="" qname="{http://services.conceptrecognizer.lumc.nl/}stringDoubleTuple"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="queryConceptID" qname="stringDoubleTuple&gt;queryConceptID" /><s:basetype optional="true" unbounded="false" typename="double" name="score" qname="stringDoubleTuple&gt;score" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFilter_List_of_Strings_by_regexstringlist1regex0filteredlist11net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true regex 0 'text/plain' java.lang.String true filteredlist 1 l('text/plain') 1 workflow org.embl.ebi.escience.scuflworkers.java.FilterStringList net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeText_constantvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity ^\S+$ net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_Listinputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity inputlist 2 l(l('')) [B true outputlist 1 l('') 1 workflow org.embl.ebi.escience.scuflworkers.java.FlattenList net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetSimilarConceptProfilesPredefinedparametersgetSimilarConceptProfilesPredefined_inputoutputgetSimilarConceptProfilesPredefined_inputcutoffValueCutoffgetSimilarConceptProfilesPredefined_inputconceptSetIdMatch_concept_setgetSimilarConceptProfilesPredefined_inputqueryConceptProfileListQuery_concept_IDgetSimilarConceptProfilesPredefined_outputinputgetSimilarConceptProfilesPredefinedparametersgetSimilarConceptProfilesPredefined_returninputgetSimilarConceptProfilesPredefined_outputreturnreturn_SimilarityScoreListsinputgetSimilarConceptProfilesPredefined_returnSimilarityScoreListsSimilarityScoreLists_SimilarityScoreListsinputreturn_SimilarityScoreListsSimilarityScoreListsSimilarityScoreLists_QueryScoreTupleListinputSimilarityScoreLists_SimilarityScoreListsQueryScoreTupleListFilter_List_of_Strings_by_regexstringlistSimilarityScoreLists_QueryScoreTupleListqueryConceptIDFilter_List_of_Strings_by_regexregexText_constantvalueFlatten_ListinputlistFilter_List_of_Strings_by_regexfilteredlistMatch_concept_IDgetSimilarConceptProfilesPredefined_returnMatchConceptProfileListSimilarity_scoregetSimilarConceptProfilesPredefined_returnSummedSimilarityScoreListQuery_concept_IDFlatten_Listoutputlist b1cb0809-a3ea-49f0-8261-4f09ec42d094 2013-02-06 13:52:40.391 UTC cc6b35c6-0d92-4ef7-ae5b-08eab3af670c 2013-01-07 13:21:45.613 UTC dafd97bb-bd4c-4540-b335-d9cfe2d84108 2012-04-16 15:04:13.913 UTC 6abd5004-cd71-47bb-8619-fe764fbe1a8c 2013-02-06 13:57:55.835 UTC 8bdb17e0-10d5-42c5-9649-595b5b3ca226 2012-09-04 11:16:15.351 UTC 46181b16-64e9-40aa-8dde-b32a9478fe1d 2011-09-27 15:29:17.819 UTC fafb8d94-026f-4044-b3ce-866fc199229b 2011-09-28 12:06:54.60 UTC 680aa556-740a-433c-b63e-82a270a9d9e3 2013-01-29 15:48:25.704 UTC 0c468adb-8c4b-4f37-839e-6d2fe21d821b 2013-02-06 13:58:23.234 UTC ae37940d-e39c-43c2-80bf-512e60710201 2012-04-16 12:45:48.511 UTC 98159653-b95c-4a97-b6b3-b400a68f0dc4 2013-01-29 14:17:24.662 UTC Authors: Kristina Hettne, Marco Roos Contributors: Reinout van Schouwen 2012-06-24 20:56:28.572 UTC 1d5bb33c-d18f-4d9c-9ead-487ab5271b7a 2011-09-27 15:37:33.997 UTC 19844d48-41a3-49e5-8cd3-5c3ccc40ec00 2013-01-07 13:19:35.160 UTC 5b1481fe-3fb7-4dfd-b527-d97b56503506 2013-02-06 12:47:43.7 UTC 33f8a974-4c7a-4f27-93f7-a4eb2ed293d4 2013-02-06 13:56:08.836 UTC 487ca7a4-63fa-45f9-baab-8f9a053ca9d0 2012-04-16 12:50:38.225 UTC 60d3ffca-7a97-485f-a391-6f8273236e1c 2013-02-01 11:26:19.951 UTC 233c6660-ebf6-47c8-af02-b1884424153d 2012-09-11 12:12:26.526 UTC a78cb530-6e91-48ac-8d8b-e6bc9ce7b0fa 2013-01-29 14:25:31.386 UTC e3d98432-1b19-474a-8c12-ed90f6aa23e8 2013-02-05 20:13:04.448 UTC 91ab33da-4da0-4e22-9542-7994c993b96a 2013-01-29 16:08:36.560 UTC 4eb7b1fd-ec11-4fff-8a9b-ed9602b6bf8d 2013-02-05 20:16:31.628 UTC 0dcad6f0-b77c-4d5d-ae1b-893a7b2436a6 2011-09-28 12:12:42.334 UTC da482794-4042-408d-adc4-c035dcb831ab 2012-04-16 12:41:12.260 UTC 6036660d-2ac0-4369-a7f7-d208a0a26265 2012-09-11 12:31:12.75 UTC 0d2ee2ad-e803-4529-afc2-e15bcd124a0c 2013-01-29 14:14:04.577 UTC 3869f1dd-8db7-4881-b73a-4d55c99c6089 2013-02-01 15:53:09.746 UTC 09430282-326d-4c5b-85a8-28ddfc97753e 2011-09-27 15:31:47.87 UTC abf2582f-e23f-40ff-b26a-c51da6f9e8f5 2013-02-05 11:11:56.753 UTC 25ac05cb-87b1-4cee-926a-4fb5c6662b8f 2013-02-05 20:18:50.908 UTC 788f406a-4ccf-40ce-82e0-cf5aad916978 2013-02-06 12:40:31.874 UTC 681cb800-d7cb-4786-8c64-585df6b607c7 2013-02-05 19:53:51.192 UTC e7d32565-d838-4bd0-987d-f03c4093d345 2013-01-29 14:21:26.174 UTC 526ee9ee-6592-4472-90d4-f392659ea584 2013-01-29 12:44:50.692 UTC ffd57175-7b65-4edb-9086-42bad4170b46 2011-09-27 13:41:33.82 UTC 4d330136-ca78-4fa0-ad95-0d34b85f8a76 2011-09-20 15:56:44.26 UTC 477ba81b-f13d-41f2-ba19-e19f6104e36e 2012-09-11 12:14:41.164 UTC e48487a3-446f-42a1-9fcc-d820a9498ff0 2012-07-18 13:14:50.306 UTC Match concept profiles with predefined set 2013-01-07 13:20:03.887 UTC abeb3495-f850-47e4-bc90-018b36584092 2011-09-28 12:24:29.380 UTC 9e39fe6a-c3da-4e04-a3ee-8c8dee6aa916 2013-01-28 15:31:38.841 UTC de3149d9-6f9a-49cd-a542-91c18f65109d 2012-09-11 12:27:01.860 UTC 494bf485-3d60-4900-88f6-060f54ef3969 2013-01-29 13:27:18.126 UTC 9a1764af-8145-4c13-a849-38a031e6f2dd 2011-09-28 12:26:45.132 UTC Purpose of workflow: The workflow can be used to match a set of concept profiles with another set of concept profiles. The result is a list of concepts ordered by their match to the query concept profiles. The workflow matches two sets of concept profiles. At the time of writing the concepts are derived from human, rat, and mouse terminologies, ontologies, and database identifiers. The profiles are lists of concepts ranked by their association with the identifying concept, as determined by co-location statistics computed from MedLine (up until 2009 at the time of writing). Author's comments: This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery. 2012-09-11 12:07:27.213 UTC dacab209-3218-4181-a2f4-eaacfb1022b1 2013-02-04 10:17:42.374 UTC 0e2bcc6a-21cb-4a66-a50c-42fd8b2226aa 2013-01-07 13:15:58.306 UTC 843e31e3-bf17-4604-a2b6-d3ff38107f9f 2013-02-06 13:57:05.208 UTC 55a9d4ab-19ee-4042-bf3d-5fabb52a3ab2 2012-06-24 20:56:30.877 UTC 7986f41c-7556-45d9-bcb3-f557b69f3acc 2012-04-15 20:28:43.911 UTC 1b7115f7-7832-4081-88df-c6ce4775238f 2011-09-28 11:35:31.328 UTC 15145a87-30e2-4e04-97a9-10572ff64aae 2011-09-28 11:37:06.330 UTC ea38018e-ee90-4ccb-ab8e-78eeec907cad 2011-09-28 12:02:39.57 UTC dacab209-3218-4181-a2f4-eaacfb1022b1 2013-02-05 11:18:43.126 UTC c55d2bf1-a3b9-46b1-a486-97b4b03eca20 2012-04-16 15:03:34.648 UTC Get_concept_informatConcept_ID00 http://rdf.biosemantics.org/owl/concept#3092619 2013-02-05 20:07:38.791 UTC Concept ID of the concept to retrieve name and definition for. 2012-07-04 11:50:31.405 UTC Concept_name GLS2 2012-07-04 11:55:50.464 UTC The name of the concept. 2012-07-04 11:51:39.675 UTC getConceptProfileparameters0parameters00 This Web service returns the concept profile for a given concept ID. 2012-09-11 12:51:04.847 UTC net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivity http://ws.biosemantics.org/ConceptRecognizerService?wsdl getConceptProfile net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetConceptProfile_inputconceptId0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity conceptId 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="getConceptProfile" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}getConceptProfile"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptId" qname="getConceptProfile&gt;conceptId" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetConceptProfile_outputinput0return00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false return 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getConceptProfileResponse" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}getConceptProfileResponse"><s:elements><s:complextype optional="true" unbounded="false" typename="conceptProfileWrapper" name="return" qname="getConceptProfileResponse&gt;return"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptId" qname="conceptProfileWrapper&gt;conceptId" /><s:basetype optional="true" unbounded="false" typename="string" name="name" qname="conceptProfileWrapper&gt;name" /><s:basetype optional="true" unbounded="false" typename="string" name="definition" qname="conceptProfileWrapper&gt;definition" /><s:arraytype optional="true" unbounded="false" wrapped="true" typename="&gt;conceptProfileWrapper&gt;ConceptVector" name="ConceptVector" qname="conceptProfileWrapper&gt;ConceptVector"><s:elementtype><s:complextype optional="false" unbounded="false" typename="stringDoubleTuple" name="" qname="{http://services.conceptrecognizer.lumc.nl/}stringDoubleTuple"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="queryConceptID" qname="stringDoubleTuple&gt;queryConceptID" /><s:basetype optional="true" unbounded="false" typename="double" name="score" qname="stringDoubleTuple&gt;score" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetConceptProfile_returninput0name00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false conceptId 0 'text/plain' 0 name 0 'text/plain' 0 definition 0 'text/plain' 0 ConceptVector 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="true" unbounded="false" typename="conceptProfileWrapper" name="return" qname="getConceptProfileResponse&gt;return"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptId" qname="conceptProfileWrapper&gt;conceptId" /><s:basetype optional="true" unbounded="false" typename="string" name="name" qname="conceptProfileWrapper&gt;name" /><s:basetype optional="true" unbounded="false" typename="string" name="definition" qname="conceptProfileWrapper&gt;definition" /><s:arraytype optional="true" unbounded="false" wrapped="true" typename="&gt;conceptProfileWrapper&gt;ConceptVector" name="ConceptVector" qname="conceptProfileWrapper&gt;ConceptVector"><s:elementtype><s:complextype optional="false" unbounded="false" typename="stringDoubleTuple" name="" qname="{http://services.conceptrecognizer.lumc.nl/}stringDoubleTuple"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="queryConceptID" qname="stringDoubleTuple&gt;queryConceptID" /><s:basetype optional="true" unbounded="false" typename="double" name="score" qname="stringDoubleTuple&gt;score" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetConceptProfileparametersgetConceptProfile_inputoutputgetConceptProfile_inputconceptIdConcept_IDgetConceptProfile_outputinputgetConceptProfileparametersgetConceptProfile_returninputgetConceptProfile_outputreturnConcept_namegetConceptProfile_returnname 6a41503c-d915-4eac-998e-0d10ee8f32f1 2013-02-05 20:07:44.871 UTC dea60608-70c7-4cf0-a8da-8513eb1a440a 2012-09-04 11:17:36.783 UTC a2ecda87-b5b6-473a-af29-b9fcf32ea707 2012-09-11 12:40:55.902 UTC Get concept information 2012-07-04 11:53:15.951 UTC Creator: Kristina Hettne on behalf of the BioSemantics group Contributions: Web services by Reinout van Schouwen 2012-07-18 13:22:40.527 UTC 04d2b539-0ecf-47a2-b036-73e97581556f 2012-07-04 11:56:13.312 UTC 2824bc65-af91-41c0-8912-e24151314a57 2012-09-11 12:51:06.419 UTC e68e4b96-f69b-4847-a2fc-eb939e3d146e 2013-02-06 14:15:07.963 UTC The workflow takes a concept ID as input and returns the ID, definition and name of the concept. This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery. 2012-07-18 13:22:23.330 UTC be71b208-25eb-473e-938d-4ad108bb3a29 2013-02-06 14:16:04.795 UTC 80bc71ed-b511-4824-98e2-3e5add19aaae 2012-09-07 14:29:24.729 UTC 3afe257a-1246-4267-be82-ccb4203af53f 2013-02-04 14:49:02.214 UTC c6eaa639-5ee7-474e-9dbb-401927d65030 2012-09-11 12:49:35.323 UTC 0f9f0834-7609-4af4-b3dd-6a9452cda123 2012-09-11 12:44:40.991 UTC b31a4602-eda2-485b-ad82-07db5fe82068 2012-07-04 11:54:39.48 UTC cf644a3e-3942-4c42-b8c7-2f834fd110d4 2012-07-18 13:22:54.983 UTC 4b5150df-f12d-4f9a-a51e-a655e4c3cba1 2013-02-04 14:41:45.41 UTC