Match_gene_lists_basmatchEntrezGenes_CSV00
List of Entrez Gene identifiers (number only) separated by comma's (nothing else), e.g. 3065,2146 for HDAC1,EZH2. The service is currently limited to rat, human, and mouse.
2012-04-24 23:32:51.391 UTC
3065,2146
2012-04-25 00:15:43.266 UTC
queryEntrezGenes_CSV00
3064
2012-04-24 23:30:03.531 UTC
Entrez gene list to match the gene list against, e.g. 3064 for HTT
2012-04-24 23:29:52.364 UTC
maxMatchesToReport00
Maximum number of concepts to report after matching the concept lists.
2012-04-24 23:58:11.388 UTC
10
2012-04-16 13:21:00.62 UTC
maxNrToExplain00
10
2012-04-16 13:23:50.360 UTC
Maximum number of concepts to explain.
2012-04-16 13:24:04.568 UTC
TopMatchingConcepts
Matching concepts ordered by matching score. The number of concepts is determined by the given maximum number of matching concepts (maxMatchesToReport).
2012-04-24 23:57:41.175 UTC
TopContributingConcepts
Ordered list of concepts that may explain the matching score for a concept-concept association. The reported number of concepts is limited by the given maximum (maxNrToExplain).
2012-04-25 00:03:35.73 UTC
SummedSimilarityScoreCommonIDTopConcepts
Common identifier for matching concepts (identifier by which the concept is also referred to by)
2012-04-25 00:02:08.80 UTC
TopMatchingConcepts_hrefExplain_concept_scoresmaxNrResults0matchConcept0queryConceptSet1ConceptName11net.sf.taverna.t2.activitiesdataflow-activity1.4-SNAPSHOTnet.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
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net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeMatch_concept_profilesCutoff0MatchConceptSet1QueryConceptSet1MatchResultList11MatchConceptID11SummedSimilarityScore11net.sf.taverna.t2.activitiesdataflow-activity1.4-SNAPSHOTnet.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSplitCSV2string0regex0split11net.sf.taverna.t2.activitieslocalworker-activity1.4-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivity
string
0
'text/plain'
java.lang.String
true
regex
0
'text/plain'
java.lang.String
true
split
1
l('text/plain')
1
workflow
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregex_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity
,
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemapConceptIdToDatabasesparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4-SNAPSHOTnet.sf.taverna.t2.activities.wsdl.WSDLActivity
http://ws.biosemantics.org/ConceptRecognizerService?wsdl
mapConceptIdToDatabases
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemapConceptIdToDatabases_inputconceptId0output00net.sf.taverna.t2.activitieswsdl-activity1.4-SNAPSHOTnet.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="mapConceptIdToDatabases" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}mapConceptIdToDatabases"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptId" qname="mapConceptIdToDatabases>conceptId" /></s:elements></s:complextype></s:extensions>
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
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0
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemapConceptIdToDatabases_outputinput0return00net.sf.taverna.t2.activitieswsdl-activity1.4-SNAPSHOTnet.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="mapConceptIdToDatabasesResponse" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}mapConceptIdToDatabasesResponse"><s:elements><s:complextype optional="true" unbounded="false" typename="databaseIDsWrapper" name="return" qname="mapConceptIdToDatabasesResponse>return"><s:elements><s:arraytype optional="true" unbounded="false" wrapped="true" typename=">databaseIDsWrapper>databaseIdList" name="databaseIdList" qname="databaseIDsWrapper>databaseIdList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="databaseIDWrapper" name="" qname="{http://services.conceptrecognizer.lumc.nl/}databaseIDWrapper"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="database" qname="databaseIDWrapper>database" /><s:basetype optional="true" unbounded="false" typename="string" name="ID" qname="databaseIDWrapper>ID" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:elements></s:complextype></s:extensions>
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
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net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemapConceptIdToDatabases_returninput0databaseIdList00net.sf.taverna.t2.activitieswsdl-activity1.4-SNAPSHOTnet.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity
input
0
'text/xml'
java.lang.String
false
databaseIdList
0
'text/xml'
0
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="true" unbounded="false" typename="databaseIDsWrapper" name="return" qname="mapConceptIdToDatabasesResponse>return"><s:elements><s:arraytype optional="true" unbounded="false" wrapped="true" typename=">databaseIDsWrapper>databaseIdList" name="databaseIdList" qname="databaseIDsWrapper>databaseIdList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="databaseIDWrapper" name="" qname="{http://services.conceptrecognizer.lumc.nl/}databaseIDWrapper"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="database" qname="databaseIDWrapper>database" /><s:basetype optional="true" unbounded="false" typename="string" name="ID" qname="databaseIDWrapper>ID" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions>
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeDatabaseID_to_ConceptIDDatabaseID0IDvalue0concepts11net.sf.taverna.t2.activitiesdataflow-activity1.4-SNAPSHOTnet.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeDatabaseID_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity
EG
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
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net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeDatabaseID_to_ConceptID_2DatabaseID0IDvalue0concepts11net.sf.taverna.t2.activitiesdataflow-activity1.4-SNAPSHOTnet.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSplitCSV1string0regex0split11net.sf.taverna.t2.activitieslocalworker-activity1.4-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivity
string
0
'text/plain'
java.lang.String
true
regex
0
'text/plain'
java.lang.String
true
split
1
l('text/plain')
1
workflow
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
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net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokereturn_databaseIdListinput0databaseIdList11net.sf.taverna.t2.activitieswsdl-activity1.4-SNAPSHOTnet.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity
input
0
'text/xml'
java.lang.String
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databaseIdList
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=">databaseIDsWrapper>databaseIdList" name="databaseIdList" qname="databaseIDsWrapper>databaseIdList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="databaseIDWrapper" name="" qname="{http://services.conceptrecognizer.lumc.nl/}databaseIDWrapper"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="database" qname="databaseIDWrapper>database" /><s:basetype optional="true" unbounded="false" typename="string" name="ID" qname="databaseIDWrapper>ID" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:extensions>
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokedatabaseIdList_databaseIdListinput0database00ID00net.sf.taverna.t2.activitieswsdl-activity1.4-SNAPSHOTnet.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity
input
0
'text/xml'
java.lang.String
false
database
0
'text/plain'
0
ID
0
'text/plain'
0
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="databaseIDWrapper" name="" qname="{http://services.conceptrecognizer.lumc.nl/}databaseIDWrapper"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="database" qname="databaseIDWrapper>database" /><s:basetype optional="true" unbounded="false" typename="string" name="ID" qname="databaseIDWrapper>ID" /></s:elements></s:complextype></s:extensions>
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeConcatenate_two_stringsstring20string10string30output00net.sf.taverna.t2.activitieslocalworker-activity1.4-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivity
string1
0
'text/plain'
java.lang.String
true
string2
0
'text/plain'
java.lang.String
true
string3
0
text/plain
java.lang.String
true
output
0
0
workflow
org.embl.ebi.escience.scuflworkers.java.StringConcat
UserNameHere
2012-04-24 23:49:32.351 UTC
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokecolonvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity
:
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeparseURLurl0output_html00output_text00net.sf.taverna.t2.activitieslocalworker-activity1.4-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivity
url
0
'text/plain'
java.lang.String
true
output_text
0
0
output_html
0
0
workflow
org.embl.ebi.escience.scuflworkers.java.StringConcat
UserNameHere
2012-04-25 07:25:02.415 UTC
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExplain_concept_scoresmaxNrResultsExplain_concept_scoresmatchConceptExplain_concept_scoresqueryConceptSetMatch_concept_profilesCutoffMatch_concept_profilesMatchConceptSetMatch_concept_profilesQueryConceptSetSplitCSV2stringSplitCSV2regexmapConceptIdToDatabasesparametersmapConceptIdToDatabases_inputconceptIdmapConceptIdToDatabases_outputinputmapConceptIdToDatabases_returninputDatabaseID_to_ConceptIDDatabaseIDDatabaseID_to_ConceptIDIDvalueDatabaseID_to_ConceptID_2DatabaseIDDatabaseID_to_ConceptID_2IDvalueSplitCSV1stringSplitCSV1regexreturn_databaseIdListinputdatabaseIdList_databaseIdListinputConcatenate_two_stringsstring2Concatenate_two_stringsstring1Concatenate_two_stringsstring3parseURLurlTopMatchingConceptsTopContributingConceptsSummedSimilarityScoreCommonIDTopConceptsTopMatchingConcepts_href
a5cea301-3dea-4e92-9952-d92bb823c283
2012-04-25 07:35:58.781 UTC
3998536c-ba30-4da2-b5aa-fcf20cffac29
2012-04-25 00:30:40.454 UTC
6576de34-7532-4585-ad77-9bf5e7441d0d
2012-04-16 15:13:38.602 UTC
0f302f1f-fb5e-4a98-aab8-f5019742e84a
2012-04-16 15:04:40.107 UTC
fca39b22-706e-4cfe-a3a9-cab391b7dd78
2012-04-17 10:46:16.632 UTC
0ac49425-8699-4745-ae7d-fe01a0274d62
2012-04-16 13:23:07.226 UTC
149af512-b6e1-4ffb-ba15-46b6f6a30a76
2012-04-24 23:37:53.678 UTC
28d4c903-6ba1-4ea3-8acc-34343191d869
2012-04-16 13:28:03.120 UTC
4358fb3d-0798-4d38-9b27-2f8fd9943f1c
2012-04-16 13:33:38.858 UTC
dfd72ed2-51d6-4219-ae44-2d66dd04082c
2012-04-24 23:35:58.111 UTC
7cc60038-fdf2-4a7d-a57f-7af1fc3c3328
2012-04-24 23:50:55.705 UTC
513fb000-c883-4834-8531-95be4fbb258d
2012-04-16 15:47:16.322 UTC
[THIS WORKFLOW IS IN BETA STAGE]
This workflow computes the match between two lists of Entrez Gene Identifiers by means of concept profile matching (Jelier et al., van Haagen et al.). The result of this is a list of concepts ordered by their matching score (the length of the list set by maxMatchNr). Of this list the summed scores are explained by computing the concepts that contribute most to the combination of the matching genes.
Example to explain (by analogy):
When a group of informaticians is matched against biology, the informaticians working in biology may be ranked on top, while the most enriched concept among such an informatician and biology may be 'bioinformatics'.
2012-04-25 00:28:37.374 UTC
0f80097e-7c50-4066-94bf-c79be990d6d0
2012-04-25 07:27:58.428 UTC
7afb2b42-68a7-4d3c-b64d-da0aceddf827
2012-04-25 00:03:44.836 UTC
4ab65d8d-aa08-4045-9f91-8ead942feb1c
2012-04-24 23:44:13.355 UTC
Marco Roos on behalf of the BioSemantics group
2012-04-17 08:32:53.985 UTC
b5c2bfcc-baaf-4249-b313-a81fa3a1c11e
2012-04-24 23:52:52.110 UTC
9cb6f657-6ddc-4209-98b5-9f2ab3586f1f
2012-04-16 16:03:29.10 UTC
1b30020f-679b-469b-9e9b-dbf477b32683
2012-04-24 13:54:33.381 UTC
5c4f140e-14a8-47b9-9775-af75fbd1652a
2012-04-16 13:25:07.600 UTC
10a75176-3a57-47a3-89bd-3845306de89f
2012-04-25 00:15:48.897 UTC
Match gene lists based on information in literature
2012-04-25 00:27:37.345 UTC
22ab0cbf-79cd-466b-9038-c39f7bd754e4
2012-04-24 14:16:12.598 UTC
3798ca3e-7639-4b4a-8fa5-5ffe6420d49c
2012-04-17 08:27:54.811 UTC
fc7f01a1-0ee9-452f-bbdd-f5420ee6ace7
2012-04-17 08:47:28.621 UTC
5db4cc03-ef86-4b3a-bfa1-f1591b88279e
2012-04-16 15:10:24.591 UTC
1989fda4-f4fc-4d56-8fc8-e89093e656c1
2012-04-25 07:31:37.982 UTC
DatabaseID_to_ConceptIDDatabaseID00
Identifier for databases, e.g. EG for Entrez Gene
2012-04-24 23:16:31.654 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
2012-04-24 23:18:17.604 UTC
concepts
Concept Identifiers for the given input, e.g. 3097212 for EG.3064
2012-04-24 23:19:16.717 UTC
3097212
2012-04-24 23:19:25.744 UTC
mapDatabaseIDToConceptIDsparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4-SNAPSHOTnet.sf.taverna.t2.activities.wsdl.WSDLActivity
http://ws.biosemantics.org/ConceptRecognizerService?wsdl
mapDatabaseIDToConceptIDs
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemapDatabaseIDToConceptIDs_inputdatabase0ID0output00net.sf.taverna.t2.activitieswsdl-activity1.4-SNAPSHOTnet.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>database" /><s:basetype optional="true" unbounded="false" typename="string" name="ID" qname="mapDatabaseIDToConceptIDs>ID" /></s:elements></s:complextype></s:extensions>
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemapDatabaseIDToConceptIDs_outputinput0return00net.sf.taverna.t2.activitieswsdl-activity1.4-SNAPSHOTnet.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="conceptIDsWrapper" name="return" qname="mapDatabaseIDToConceptIDsResponse>return"><s:elements><s:arraytype optional="true" unbounded="false" wrapped="true" typename=">conceptIDsWrapper>conceptIDset" name="conceptIDset" qname="conceptIDsWrapper>conceptIDset"><s:elementtype><s:basetype optional="false" unbounded="false" typename="int" name="" qname="{http://www.w3.org/2001/XMLSchema}int" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:elements></s:complextype></s:extensions>
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemapDatabaseIDToConceptIDs_returninput0conceptIDset11net.sf.taverna.t2.activitieswsdl-activity1.4-SNAPSHOTnet.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity
input
0
'text/xml'
java.lang.String
false
conceptIDset
1
l('text/plain')
1
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="true" unbounded="false" typename="conceptIDsWrapper" name="return" qname="mapDatabaseIDToConceptIDsResponse>return"><s:elements><s:arraytype optional="true" unbounded="false" wrapped="true" typename=">conceptIDsWrapper>conceptIDset" name="conceptIDset" qname="conceptIDsWrapper>conceptIDset"><s:elementtype><s:basetype optional="false" unbounded="false" typename="int" name="" qname="{http://www.w3.org/2001/XMLSchema}int" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions>
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemapDatabaseIDToConceptIDsparametersmapDatabaseIDToConceptIDs_inputdatabasemapDatabaseIDToConceptIDs_inputIDmapDatabaseIDToConceptIDs_outputinputmapDatabaseIDToConceptIDs_returninputconcepts
Marco Roos on behalf of the BioSemantics group
Web Service by Reinout van Schouwen
2012-04-24 23:22:11.86 UTC
0b447fad-9299-453c-9195-e00c9fb687a7
2012-04-24 23:20:02.840 UTC
c2cbb1b4-e2b2-4c45-9dfd-5323f702be83
2012-04-24 23:22:49.83 UTC
80ee33e8-dddc-4d0f-aef9-ce9790e69904
2012-04-24 23:12:44.984 UTC
DatabaseID_to_ConceptID
2012-04-24 23:22:45.412 UTC
Match_concept_profilesCutoff00
25
2011-09-27 13:18:52.151 UTC
The number of resulting matched concepts that will be shown.
2012-04-16 12:36:29.53 UTC
MatchConceptSet11
The ConceptSet that is to be matched. For example a list consisting of concept ids: 3088049, 3088115, 3089563, 3090191, 3092619, 3094840, 3098813, 3103320, 3103643, 3108241, 3109737
2012-04-16 12:38:17.919 UTC
3088049
2012-04-16 12:38:41.720 UTC
QueryConceptSet11
The ConceptSet (a list of concept identifiers) to be queried. For example: 4275360
2012-04-16 12:39:57.499 UTC
4275360
2012-04-16 12:39:21.505 UTC
MatchResultListSimilarityScoreSummedSimilarityScoreMatchConceptIDgetSimilarConceptProfilesparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4-SNAPSHOTnet.sf.taverna.t2.activities.wsdl.WSDLActivity
http://ws.biosemantics.org/ConceptRecognizerService?wsdl
getSimilarConceptProfiles
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetSimilarConceptProfiles_inputcutoffValue0queryConceptProfileList1matchConceptProfileList1output00net.sf.taverna.t2.activitieswsdl-activity1.4-SNAPSHOTnet.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity
cutoffValue
0
'text/plain'
false
matchConceptProfileList
1
l('text/plain')
false
queryConceptProfileList
1
l('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="getSimilarConceptProfiles" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}getSimilarConceptProfiles"><s:elements><s:basetype optional="false" unbounded="false" typename="int" name="cutoffValue" qname="getSimilarConceptProfiles>cutoffValue" /><s:arraytype optional="true" unbounded="true" wrapped="false" typename="int" name="matchConceptProfileList" qname="getSimilarConceptProfiles>matchConceptProfileList"><s:elementtype><s:basetype optional="false" unbounded="false" typename="int" name="" qname="{http://www.w3.org/2001/XMLSchema}int" /></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="true" wrapped="false" typename="int" name="queryConceptProfileList" qname="getSimilarConceptProfiles>queryConceptProfileList"><s:elementtype><s:basetype optional="false" unbounded="false" typename="int" name="" qname="{http://www.w3.org/2001/XMLSchema}int" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions>
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetSimilarConceptProfiles_outputinput0MatchingResult00net.sf.taverna.t2.activitieswsdl-activity1.4-SNAPSHOTnet.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity
input
0
'text/xml'
java.lang.String
false
MatchingResult
0
'text/xml'
0
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getSimilarConceptProfilesResponse" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}getSimilarConceptProfilesResponse"><s:elements><s:complextype optional="true" unbounded="false" typename="matchingResult" name="MatchingResult" qname="getSimilarConceptProfilesResponse>MatchingResult"><s:elements><s:arraytype optional="true" unbounded="false" wrapped="true" typename=">matchingResult>MatchConceptProfileList" name="MatchConceptProfileList" qname="matchingResult>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>SimilarityScoreLists"><s:elementtype><s:arraytype optional="false" unbounded="false" wrapped="true" typename="scoreListImpl" name="ArrayOfdouble" qname="{http://services.conceptrecognizer.lumc.nl/}scoreListImpl"><s:elementtype><s:basetype optional="false" unbounded="false" typename="double" name="" qname="{http://www.w3.org/2001/XMLSchema}double" /></s:elementtype></s:arraytype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename=">matchingResult>SummedSimilarityScoreList" name="SummedSimilarityScoreList" qname="matchingResult>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-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetSimilarConceptProfiles_MatchingResultinput0MatchConceptProfileList11SimilarityScoreLists00SummedSimilarityScoreList11net.sf.taverna.t2.activitieswsdl-activity1.4-SNAPSHOTnet.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="MatchingResult" qname="getSimilarConceptProfilesResponse>MatchingResult"><s:elements><s:arraytype optional="true" unbounded="false" wrapped="true" typename=">matchingResult>MatchConceptProfileList" name="MatchConceptProfileList" qname="matchingResult>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>SimilarityScoreLists"><s:elementtype><s:arraytype optional="false" unbounded="false" wrapped="true" typename="scoreListImpl" name="ArrayOfdouble" qname="{http://services.conceptrecognizer.lumc.nl/}scoreListImpl"><s:elementtype><s:basetype optional="false" unbounded="false" typename="double" name="" qname="{http://www.w3.org/2001/XMLSchema}double" /></s:elementtype></s:arraytype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename=">matchingResult>SummedSimilarityScoreList" name="SummedSimilarityScoreList" qname="matchingResult>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-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFilter_ConceptIDregex0group0stringlist1filteredlist11net.sf.taverna.t2.activitieslocalworker-activity1.4-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivity
stringlist
1
l('text/plain')
java.lang.String
true
regex
0
'text/plain'
java.lang.String
true
group
0
'text/plain'
java.lang.String
true
filteredlist
1
l('text/plain')
1
workflow
org.embl.ebi.escience.scuflworkers.java.RegularExpressionStringList
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregex_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity
<http://rdf.biosemantics.org/owl/concept#(.+)/>
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokegroup_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetSimilarConceptProfilesparametersgetSimilarConceptProfiles_inputcutoffValuegetSimilarConceptProfiles_inputqueryConceptProfileListgetSimilarConceptProfiles_inputmatchConceptProfileListgetSimilarConceptProfiles_outputinputgetSimilarConceptProfiles_MatchingResultinputFilter_ConceptIDregexFilter_ConceptIDgroupFilter_ConceptIDstringlistMatchResultListSimilarityScoreSummedSimilarityScoreMatchConceptID
46181b16-64e9-40aa-8dde-b32a9478fe1d
2011-09-27 15:29:17.819 UTC
dafd97bb-bd4c-4540-b335-d9cfe2d84108
2012-04-16 15:04:13.913 UTC
fafb8d94-026f-4044-b3ce-866fc199229b
2011-09-28 12:06:54.60 UTC
1d5bb33c-d18f-4d9c-9ead-487ab5271b7a
2011-09-27 15:37:33.997 UTC
15145a87-30e2-4e04-97a9-10572ff64aae
2011-09-28 11:37:06.330 UTC
09430282-326d-4c5b-85a8-28ddfc97753e
2011-09-27 15:31:47.87 UTC
da482794-4042-408d-adc4-c035dcb831ab
2012-04-16 12:41:12.260 UTC
abeb3495-f850-47e4-bc90-018b36584092
2011-09-28 12:24:29.380 UTC
0dcad6f0-b77c-4d5d-ae1b-893a7b2436a6
2011-09-28 12:12:42.334 UTC
Match concept profiles
2011-09-28 11:31:19.752 UTC
ffd57175-7b65-4edb-9086-42bad4170b46
2011-09-27 13:41:33.82 UTC
9a1764af-8145-4c13-a849-38a031e6f2dd
2011-09-28 12:26:45.132 UTC
1b7115f7-7832-4081-88df-c6ce4775238f
2011-09-28 11:35:31.328 UTC
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.
2012-04-16 12:50:01.68 UTC
7986f41c-7556-45d9-bcb3-f557b69f3acc
2012-04-15 20:28:43.911 UTC
4d330136-ca78-4fa0-ad95-0d34b85f8a76
2011-09-20 15:56:44.26 UTC
ae37940d-e39c-43c2-80bf-512e60710201
2012-04-16 12:45:48.511 UTC
ea38018e-ee90-4ccb-ab8e-78eeec907cad
2011-09-28 12:02:39.57 UTC
c55d2bf1-a3b9-46b1-a486-97b4b03eca20
2012-04-16 15:03:34.648 UTC
Kristina Hettne
2011-09-28 11:30:59.360 UTC
487ca7a4-63fa-45f9-baab-8f9a053ca9d0
2012-04-16 12:50:38.225 UTC
Explain_concept_scoresmatchConcept00
79822
2012-04-16 12:58:11.409 UTC
Concept Profile list (by concept identifier). Examples 79822, 25362
2012-04-16 12:57:59.976 UTC
maxNrResults00
Maximum number of concepts to return.
2012-04-16 13:04:21.46 UTC
10
2012-04-16 13:04:29.375 UTC
queryConceptSet11ConceptNameConceptIDConceptContributionxml_tablereturn_ConceptContributionTableinput0ConceptContributionTable11net.sf.taverna.t2.activitieswsdl-activity1.4-SNAPSHOTnet.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=">conceptContributionsWrapper>ConceptContributionTable" name="ConceptContributionTable" qname="conceptContributionsWrapper>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>conceptName" /><s:basetype optional="true" unbounded="false" typename="double" name="contribution" qname="conceptContribution>contribution" /><s:basetype optional="true" unbounded="false" typename="int" name="conceptId" qname="conceptContribution>conceptId" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:extensions>
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeConceptContributionTable_ConceptContributionTableinput0conceptId00contribution00conceptName00net.sf.taverna.t2.activitieswsdl-activity1.4-SNAPSHOTnet.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>conceptName" /><s:basetype optional="true" unbounded="false" typename="double" name="contribution" qname="conceptContribution>contribution" /><s:basetype optional="true" unbounded="false" typename="int" name="conceptId" qname="conceptContribution>conceptId" /></s:elements></s:complextype></s:extensions>
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeexplainScoresparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4-SNAPSHOTnet.sf.taverna.t2.activities.wsdl.WSDLActivity
http://ws.biosemantics.org/ConceptRecognizerService?wsdl
explainScores
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeexplainScores_inputcutoffValue0conceptCUIs1output00net.sf.taverna.t2.activitieswsdl-activity1.4-SNAPSHOTnet.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity
cutoffValue
0
'text/plain'
false
conceptCUIs
1
l('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="explainScores" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}explainScores"><s:elements><s:basetype optional="false" unbounded="false" typename="int" name="cutoffValue" qname="explainScores>cutoffValue" /><s:arraytype optional="true" unbounded="true" wrapped="false" typename="int" name="conceptCUIs" qname="explainScores>conceptCUIs"><s:elementtype><s:basetype optional="false" unbounded="false" typename="int" name="" qname="{http://www.w3.org/2001/XMLSchema}int" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions>
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeexplainScores_outputinput0return00net.sf.taverna.t2.activitieswsdl-activity1.4-SNAPSHOTnet.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="explainScoresResponse" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}explainScoresResponse"><s:elements><s:complextype optional="true" unbounded="false" typename="conceptContributionsWrapper" name="return" qname="explainScoresResponse>return"><s:elements><s:arraytype optional="true" unbounded="false" wrapped="true" typename=">conceptContributionsWrapper>ConceptContributionTable" name="ConceptContributionTable" qname="conceptContributionsWrapper>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>conceptName" /><s:basetype optional="true" unbounded="false" typename="double" name="contribution" qname="conceptContribution>contribution" /><s:basetype optional="true" unbounded="false" typename="int" name="conceptId" qname="conceptContribution>conceptId" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:elements></s:complextype></s:extensions>
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeexplainScores_returninput0ConceptContributionTable00net.sf.taverna.t2.activitieswsdl-activity1.4-SNAPSHOTnet.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="explainScoresResponse>return"><s:elements><s:arraytype optional="true" unbounded="false" wrapped="true" typename=">conceptContributionsWrapper>ConceptContributionTable" name="ConceptContributionTable" qname="conceptContributionsWrapper>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>conceptName" /><s:basetype optional="true" unbounded="false" typename="double" name="contribution" qname="conceptContribution>contribution" /><s:basetype optional="true" unbounded="false" typename="int" name="conceptId" qname="conceptContribution>conceptId" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions>
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshellitem0inputList1outputList11net.sf.taverna.t2.activitiesbeanshell-activity1.4-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivity
inputList
1
text/plain
java.lang.String
true
item
0
text/plain
java.lang.String
true
outputList
1
1
workflow
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokereturn_ConceptContributionTableinputConceptContributionTable_ConceptContributionTableinputexplainScoresparametersexplainScores_inputcutoffValueexplainScores_inputconceptCUIsexplainScores_outputinputexplainScores_returninputBeanshellitemBeanshellinputListConceptNameConceptIDConceptContributionxml_table
Creator: Reinout van Schouwen on behalf of the BIoSemantics Group
Adaptation by Marco Roos
2012-04-16 12:59:53.250 UTC
541a7a2d-e3e3-490d-885b-52d653a21d11
2012-02-03 11:42:15.89 UTC
Explain concept scores of concept profiles (enrichment with concept set)
2012-04-16 13:00:51.27 UTC
0faa8a91-3a1c-4e03-b74d-f271e7b96290
2012-04-16 12:55:56.499 UTC
Explain concept scores
2012-04-16 13:00:42.27 UTC
abaeb048-e186-4c8d-92d4-6b32b22603d8
2012-04-16 13:01:16.427 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
7a995f89-0c37-48b9-b0f7-8eca5cd36420
2012-01-06 11:51:06.790 UTC
8efd062c-22d8-4fc6-bfe4-ea8f96ba7e2a
2012-04-16 12:58:21.8 UTC
89f2da6a-161b-47b1-a048-a65fd35f912c
2012-01-06 11:47:16.46 UTC
9e4c2fcc-6dcc-46d5-9edd-d7841389ef5c
2012-04-17 08:22:27.551 UTC
bb8d1d77-e3d2-4cee-aee9-3cd4e1bd8547
2012-01-06 12:38:00.681 UTC
13050a9d-bdda-4de5-8bc7-8503457302cd
2012-04-16 13:02:36.340 UTC
fc7ae322-fcac-41c5-b136-0767d52680b0
2012-03-21 13:53:26.66 UTC
8d4a9091-0ba9-468e-9883-7b08e5212cd2
2012-04-16 13:07:32.864 UTC