Explain_concept_scoresC_ConceptID00 http://rdf.biosemantics.org/emco/v1.5/concepts/C1156814 2014-07-14 09:37:51.636 UTC The concept id of the C concept. 2012-09-11 09:01:25.824 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 The concept id of the A concept. 2012-09-11 09:01:33.736 UTC http://rdf.biosemantics.org/emco/v1.5/concepts/C3054172 2014-07-14 09:37:37.845 UTC B_ConceptName glutamine 2014-06-11 09:07:03.593 UTC The concept name of the explanatory B concept. 2012-09-11 09:01:44.136 UTC B_ConceptID The concept ID of the explanatory B concept. 2012-09-11 09:01:40.385 UTC http://rdf.biosemantics.org/emco/v1.5/concepts/C4354094 2014-07-14 09:38:48.564 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 39.47658836841583 2014-06-11 09:06:34.372 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/ConceptProfileMiningService?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 541a7a2d-e3e3-490d-885b-52d653a21d11 2012-02-03 11:42:15.89 UTC 2b762f5e-4473-4d48-b78f-df306600467a 2012-09-11 09:11:13.838 UTC 0faa8a91-3a1c-4e03-b74d-f271e7b96290 2012-04-16 12:55:56.499 UTC 4f826cfe-3950-4151-bbe6-bff67413be51 2012-09-07 15:22:15.103 UTC 142a2c6d-8e96-4c9f-ad64-da97fd4c2597 2012-09-04 11:16:44.759 UTC 8f284446-2578-4c4d-b81d-e842a463641b 2012-09-07 15:34:00.455 UTC 88e1d0d3-3377-4a21-a98f-19020444e686 2012-09-07 14:58:20.922 UTC 90f0af1e-a653-4a85-889c-4120accdd9d9 2012-09-07 14:44:36.440 UTC 3c6eca00-e3a8-46b8-86bd-7c4b48a3ac77 2012-07-18 13:20:01.872 UTC 09802e77-93ac-45ba-9ad5-e7bea33cda8b 2013-02-05 20:09:38.174 UTC a6c096b8-050d-48bf-8b9c-114762aac26d 2012-09-07 14:52:03.90 UTC d6bd7053-1886-4ca1-806c-8eabfbcaee02 2014-07-14 09:39:01.805 UTC 13050a9d-bdda-4de5-8bc7-8503457302cd 2012-04-16 13:02:36.340 UTC abaeb048-e186-4c8d-92d4-6b32b22603d8 2012-04-16 13:01:16.427 UTC f70e92dc-739d-47b9-bba3-98499064022e 2014-06-11 09:08:27.65 UTC c416805f-aa9d-4d44-b434-f253935ed0ef 2012-09-11 08:57:11.33 UTC 9a6508bd-87c3-4d9c-99f2-9003b5b57df4 2012-09-11 09:01:50.31 UTC Creator: Reinout van Schouwen on behalf of the BioSemantics Group Adaptations by Marco Roos and Kristina Hettne 2014-07-14 09:39:43.813 UTC 4bed166d-9815-4a35-a613-869b300b7973 2012-04-16 13:04:34.678 UTC fc7ae322-fcac-41c5-b136-0767d52680b0 2012-03-21 13:53:26.66 UTC 7d6ba6db-2552-4c15-b800-1789f5385d44 2012-09-07 15:18:14.352 UTC 2b5167d3-3864-46c1-b761-b66ab721da54 2012-02-03 13:52:44.748 UTC bb8d1d77-e3d2-4cee-aee9-3cd4e1bd8547 2012-01-06 12:38:00.681 UTC Explain concept scores 2012-04-16 13:00:42.27 UTC 7a995f89-0c37-48b9-b0f7-8eca5cd36420 2012-01-06 11:51:06.790 UTC 89f2da6a-161b-47b1-a048-a65fd35f912c 2012-01-06 11:47:16.46 UTC 6bab82da-54d0-4bc7-96fd-e5c5d3c6d77f 2012-09-07 14:37:53.808 UTC 8d4a9091-0ba9-468e-9883-7b08e5212cd2 2012-04-16 13:07:32.864 UTC e60ee0d1-f252-418a-afef-0b9fd6ba0112 2014-07-14 09:40:03.522 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). 2014-07-14 09:39:55.492 UTC 1ea652c5-572b-4b0a-b66d-5ae41a7b7fe1 2013-02-05 09:41:27.678 UTC 9e4c2fcc-6dcc-46d5-9edd-d7841389ef5c 2012-04-17 08:22:27.551 UTC 8efd062c-22d8-4fc6-bfe4-ea8f96ba7e2a 2012-04-16 12:58:21.8 UTC 4b937a61-6180-48ce-a679-cf3ed1c8f208 2012-09-11 08:58:54.136 UTC 713fa342-cdf4-48b7-850d-abecb37b9b1f 2012-09-11 08:58:13.328 UTC a260c127-7bbc-4dde-86a9-80647fcbb862 2012-09-10 15:18:42.957 UTC