root/LUMC_HG/HandsOn/Workflows/Marco/BioSemantics/ConceptMiningWorkflows/MatchConceptSets.t2flow @ 82

Revision 82, 162.7 KB (checked in by M.Roos1@…, 2 years ago)

New, more complete version of match concept sets. Now includes explain operation. NB Web Services still need some testing/bug fixing.

Line 
1<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="fca39b22-706e-4cfe-a3a9-cab391b7dd78" role="top"><name>Workflow7</name><inputPorts><port><name>ProteinList_CSV</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
2  <annotationAssertions>
3    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
4      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
5        <text>Q13547,P31645</text>
6      </annotationBean>
7      <date>2012-04-16 17:08:48.807 CEST</date>
8      <creators />
9      <curationEventList />
10    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
11  </annotationAssertions>
12</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
13  <annotationAssertions>
14    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
15      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
16        <text>List of uniprot identifiers separated by comma's (nothing else). The service is currently limited to rat, human, and mouse.</text>
17      </annotationBean>
18      <date>2012-04-16 17:09:27.959 CEST</date>
19      <creators />
20      <curationEventList />
21    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
22  </annotationAssertions>
23</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>queryTerm</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
24  <annotationAssertions>
25    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
26      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
27        <text>Query term to match the protein list against. E.g. Huntington's Disease, or HDAC1</text>
28      </annotationBean>
29      <date>2012-04-16 17:10:21.431 CEST</date>
30      <creators />
31      <curationEventList />
32    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
33  </annotationAssertions>
34</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
35  <annotationAssertions>
36    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
37      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
38        <text>EZH2</text>
39      </annotationBean>
40      <date>2012-04-17 12:46:10.201 CEST</date>
41      <creators />
42      <curationEventList />
43    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
44  </annotationAssertions>
45</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>cutOff</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
46  <annotationAssertions>
47    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
48      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
49        <text>10</text>
50      </annotationBean>
51      <date>2012-04-16 15:21:00.62 CEST</date>
52      <creators />
53      <curationEventList />
54    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
55  </annotationAssertions>
56</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
57  <annotationAssertions>
58    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
59      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
60        <text>cut off value for matching concept lists</text>
61      </annotationBean>
62      <date>2012-04-16 15:20:51.597 CEST</date>
63      <creators />
64      <curationEventList />
65    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
66  </annotationAssertions>
67</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>maxNrToExplain</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
68  <annotationAssertions>
69    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
70      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
71        <text>10</text>
72      </annotationBean>
73      <date>2012-04-16 15:23:50.360 CEST</date>
74      <creators />
75      <curationEventList />
76    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
77  </annotationAssertions>
78</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
79  <annotationAssertions>
80    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
81      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
82        <text>Maximum number of concepts to explain.</text>
83      </annotationBean>
84      <date>2012-04-16 15:24:04.568 CEST</date>
85      <creators />
86      <curationEventList />
87    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
88  </annotationAssertions>
89</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port></inputPorts><outputPorts><port><name>contributionTable_xml</name><annotations /></port><port><name>TopMatchingConcepts</name><annotations /></port><port><name>TopContributingConcepts</name><annotations /></port><port><name>SummedSimilarity</name><annotations /></port></outputPorts><processors><processor><name>Explain_concept_scores</name><inputPorts><port><name>maxNrResults</name><depth>0</depth></port><port><name>matchConcept</name><depth>0</depth></port><port><name>queryConceptSet</name><depth>1</depth></port></inputPorts><outputPorts><port><name>xml_table</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>ConceptName</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="queryConceptSet" to="queryConceptSet" /><map from="matchConcept" to="matchConcept" /><map from="maxNrResults" to="maxNrResults" /></inputMap><outputMap><map from="xml_table" to="xml_table" /><map from="ConceptName" to="ConceptName" /></outputMap><configBean encoding="dataflow"><dataflow ref="9e4c2fcc-6dcc-46d5-9edd-d7841389ef5c" /></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
90  <maxJobs>1</maxJobs>
91</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
92  <backoffFactor>1.0</backoffFactor>
93  <initialDelay>1000</initialDelay>
94  <maxDelay>5000</maxDelay>
95  <maxRetries>0</maxRetries>
96</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="maxNrResults" depth="0" /><port name="matchConcept" depth="0" /><port name="queryConceptSet" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Match_concept_profiles</name><inputPorts><port><name>MatchConceptSet</name><depth>1</depth></port><port><name>QueryConceptSet</name><depth>1</depth></port><port><name>Cutoff</name><depth>0</depth></port></inputPorts><outputPorts><port><name>MatchResultList</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>MatchConceptID</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>SummedSimilarityScore</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="QueryConceptSet" to="QueryConceptSet" /><map from="MatchConceptSet" to="MatchConceptSet" /><map from="Cutoff" to="Cutoff" /></inputMap><outputMap><map from="SummedSimilarityScore" to="SummedSimilarityScore" /><map from="MatchConceptID" to="MatchConceptID" /><map from="MatchResultList" to="MatchResultList" /></outputMap><configBean encoding="dataflow"><dataflow ref="dafd97bb-bd4c-4540-b335-d9cfe2d84108" /></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
97  <maxJobs>1</maxJobs>
98</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
99  <backoffFactor>1.0</backoffFactor>
100  <initialDelay>1000</initialDelay>
101  <maxDelay>5000</maxDelay>
102  <maxRetries>0</maxRetries>
103</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="MatchConceptSet" depth="1" /><port name="QueryConceptSet" depth="1" /><port name="Cutoff" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>SplitCSV</name><inputPorts><port><name>string</name><depth>0</depth></port><port><name>regex</name><depth>0</depth></port></inputPorts><outputPorts><port><name>split</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="regex" to="regex" /><map from="string" to="string" /></inputMap><outputMap><map from="split" to="split" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
104  <inputs>
105    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
106      <name>string</name>
107      <depth>0</depth>
108      <mimeTypes>
109        <string>'text/plain'</string>
110      </mimeTypes>
111      <handledReferenceSchemes />
112      <translatedElementType>java.lang.String</translatedElementType>
113      <allowsLiteralValues>true</allowsLiteralValues>
114    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
115    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
116      <name>regex</name>
117      <depth>0</depth>
118      <mimeTypes>
119        <string>'text/plain'</string>
120      </mimeTypes>
121      <handledReferenceSchemes />
122      <translatedElementType>java.lang.String</translatedElementType>
123      <allowsLiteralValues>true</allowsLiteralValues>
124    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
125  </inputs>
126  <outputs>
127    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
128      <name>split</name>
129      <depth>1</depth>
130      <mimeTypes>
131        <string>l('text/plain')</string>
132      </mimeTypes>
133      <granularDepth>1</granularDepth>
134    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
135  </outputs>
136  <classLoaderSharing>workflow</classLoaderSharing>
137  <localDependencies />
138  <artifactDependencies />
139  <script>List split = new ArrayList();
140if (!string.equals("")) {
141        String regexString = ",";
142        if (regex != void) {
143                regexString = regex;
144        }
145        String[] result = string.split(regexString);
146        for (int i = 0; i &lt; result.length; i++) {
147                split.add(result[i]);
148        }
149}
150</script>
151  <dependencies />
152  <localworkerName>org.embl.ebi.escience.scuflworkers.java.SplitByRegex</localworkerName>
153</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
154  <maxJobs>1</maxJobs>
155</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
156  <backoffFactor>1.0</backoffFactor>
157  <initialDelay>1000</initialDelay>
158  <maxDelay>5000</maxDelay>
159  <maxRetries>0</maxRetries>
160</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="string" depth="0" /><port name="regex" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>regex_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
161  <value>,</value>
162</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
163  <maxJobs>1</maxJobs>
164</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
165  <backoffFactor>1.0</backoffFactor>
166  <initialDelay>1000</initialDelay>
167  <maxDelay>5000</maxDelay>
168  <maxRetries>0</maxRetries>
169</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>getConceptIdsFromTerm</name><inputPorts><port><name>parameters</name><depth>0</depth></port></inputPorts><outputPorts><port><name>parameters</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="parameters" to="parameters" /></inputMap><outputMap><map from="parameters" to="parameters" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
170  <wsdl>http://mybiobank.org:8080/axis2/services/SynsetServer?wsdl</wsdl>
171  <operation>getConceptIdsFromTerm</operation>
172</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
173  <maxJobs>1</maxJobs>
174</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
175  <backoffFactor>1.0</backoffFactor>
176  <initialDelay>1000</initialDelay>
177  <maxDelay>5000</maxDelay>
178  <maxRetries>0</maxRetries>
179</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="parameters" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>getConceptIdsFromTerm_input</name><inputPorts><port><name>term</name><depth>0</depth></port><port><name>limit</name><depth>0</depth></port></inputPorts><outputPorts><port><name>output</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity</class><inputMap><map from="limit" to="limit" /><map from="term" to="term" /></inputMap><outputMap><map from="output" to="output" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
180  <inputs>
181    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
182      <name>term</name>
183      <depth>0</depth>
184      <mimeTypes class="java.util.Collections$SingletonList">
185        <element class="string">'text/plain'</element>
186      </mimeTypes>
187      <allowsLiteralValues>false</allowsLiteralValues>
188    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
189    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
190      <name>limit</name>
191      <depth>0</depth>
192      <mimeTypes class="java.util.Collections$SingletonList">
193        <element class="string">'text/plain'</element>
194      </mimeTypes>
195      <allowsLiteralValues>false</allowsLiteralValues>
196    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
197  </inputs>
198  <outputs>
199    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
200      <name>output</name>
201      <depth>0</depth>
202      <mimeTypes class="java.util.Collections$SingletonList">
203        <element class="string">'text/xml'</element>
204      </mimeTypes>
205      <granularDepth>0</granularDepth>
206    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
207  </outputs>
208  <wrappedTypeXML>&lt;s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"&gt;&lt;s:complextype optional="false" unbounded="false" typename="getConceptIdsFromTerm" name="parameters" qname="{http://ws.apache.org/axis2}getConceptIdsFromTerm"&gt;&lt;s:elements&gt;&lt;s:basetype optional="true" unbounded="false" typename="string" name="term" qname="{http://ws.apache.org/axis2}&amp;gt;getConceptIdsFromTerm&amp;gt;term" /&gt;&lt;s:basetype optional="true" unbounded="false" typename="int" name="limit" qname="{http://ws.apache.org/axis2}&amp;gt;getConceptIdsFromTerm&amp;gt;limit" /&gt;&lt;/s:elements&gt;&lt;/s:complextype&gt;&lt;/s:extensions&gt;</wrappedTypeXML>
209</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
210  <maxJobs>1</maxJobs>
211</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
212  <backoffFactor>1.0</backoffFactor>
213  <initialDelay>1000</initialDelay>
214  <maxDelay>5000</maxDelay>
215  <maxRetries>0</maxRetries>
216</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="term" depth="0" /><port name="limit" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>getConceptIdsFromTerm_output</name><inputPorts><port><name>input</name><depth>0</depth></port></inputPorts><outputPorts><port><name>return</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity</class><inputMap><map from="input" to="input" /></inputMap><outputMap><map from="return" to="return" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
217  <inputs>
218    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
219      <name>input</name>
220      <depth>0</depth>
221      <mimeTypes class="java.util.Collections$SingletonList">
222        <element class="string">'text/xml'</element>
223      </mimeTypes>
224      <handledReferenceSchemes />
225      <translatedElementType>java.lang.String</translatedElementType>
226      <allowsLiteralValues>false</allowsLiteralValues>
227    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
228  </inputs>
229  <outputs>
230    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
231      <name>return</name>
232      <depth>0</depth>
233      <mimeTypes class="java.util.Collections$SingletonList">
234        <element class="string">'text/plain'</element>
235      </mimeTypes>
236      <granularDepth>0</granularDepth>
237    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
238  </outputs>
239  <wrappedTypeXML>&lt;s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"&gt;&lt;s:complextype optional="false" unbounded="false" typename="getConceptIdsFromTermResponse" name="parameters" qname="{http://ws.apache.org/axis2}getConceptIdsFromTermResponse"&gt;&lt;s:elements&gt;&lt;s:basetype optional="true" unbounded="false" typename="anyType" name="return" qname="{http://ws.apache.org/axis2}&amp;gt;getConceptIdsFromTermResponse&amp;gt;return" /&gt;&lt;/s:elements&gt;&lt;/s:complextype&gt;&lt;/s:extensions&gt;</wrappedTypeXML>
240</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
241  <maxJobs>1</maxJobs>
242</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
243  <backoffFactor>1.0</backoffFactor>
244  <initialDelay>1000</initialDelay>
245  <maxDelay>5000</maxDelay>
246  <maxRetries>0</maxRetries>
247</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="input" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>getConceptIdsFromTerm_2</name><inputPorts><port><name>parameters</name><depth>0</depth></port></inputPorts><outputPorts><port><name>parameters</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="parameters" to="parameters" /></inputMap><outputMap><map from="parameters" to="parameters" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
248  <wsdl>http://mybiobank.org:8080/axis2/services/SynsetServer?wsdl</wsdl>
249  <operation>getConceptIdsFromTerm</operation>
250</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
251  <maxJobs>1</maxJobs>
252</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
253  <backoffFactor>1.0</backoffFactor>
254  <initialDelay>1000</initialDelay>
255  <maxDelay>5000</maxDelay>
256  <maxRetries>0</maxRetries>
257</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="parameters" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>queryTerm</name><inputPorts><port><name>term</name><depth>0</depth></port><port><name>limit</name><depth>0</depth></port></inputPorts><outputPorts><port><name>output</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity</class><inputMap><map from="limit" to="limit" /><map from="term" to="term" /></inputMap><outputMap><map from="output" to="output" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
258  <inputs>
259    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
260      <name>term</name>
261      <depth>0</depth>
262      <mimeTypes class="java.util.Collections$SingletonList">
263        <element class="string">'text/plain'</element>
264      </mimeTypes>
265      <allowsLiteralValues>false</allowsLiteralValues>
266    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
267    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
268      <name>limit</name>
269      <depth>0</depth>
270      <mimeTypes class="java.util.Collections$SingletonList">
271        <element class="string">'text/plain'</element>
272      </mimeTypes>
273      <allowsLiteralValues>false</allowsLiteralValues>
274    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
275  </inputs>
276  <outputs>
277    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
278      <name>output</name>
279      <depth>0</depth>
280      <mimeTypes class="java.util.Collections$SingletonList">
281        <element class="string">'text/xml'</element>
282      </mimeTypes>
283      <granularDepth>0</granularDepth>
284    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
285  </outputs>
286  <wrappedTypeXML>&lt;s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"&gt;&lt;s:complextype optional="false" unbounded="false" typename="getConceptIdsFromTerm" name="parameters" qname="{http://ws.apache.org/axis2}getConceptIdsFromTerm"&gt;&lt;s:elements&gt;&lt;s:basetype optional="true" unbounded="false" typename="string" name="term" qname="{http://ws.apache.org/axis2}&amp;gt;getConceptIdsFromTerm&amp;gt;term" /&gt;&lt;s:basetype optional="true" unbounded="false" typename="int" name="limit" qname="{http://ws.apache.org/axis2}&amp;gt;getConceptIdsFromTerm&amp;gt;limit" /&gt;&lt;/s:elements&gt;&lt;/s:complextype&gt;&lt;/s:extensions&gt;</wrappedTypeXML>
287</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
288  <maxJobs>1</maxJobs>
289</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
290  <backoffFactor>1.0</backoffFactor>
291  <initialDelay>1000</initialDelay>
292  <maxDelay>5000</maxDelay>
293  <maxRetries>0</maxRetries>
294</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="term" depth="0" /><port name="limit" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>queryConceptIdsFromTerm</name><inputPorts><port><name>input</name><depth>0</depth></port></inputPorts><outputPorts><port><name>return</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity</class><inputMap><map from="input" to="input" /></inputMap><outputMap><map from="return" to="return" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
295  <inputs>
296    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
297      <name>input</name>
298      <depth>0</depth>
299      <mimeTypes class="java.util.Collections$SingletonList">
300        <element class="string">'text/xml'</element>
301      </mimeTypes>
302      <handledReferenceSchemes />
303      <translatedElementType>java.lang.String</translatedElementType>
304      <allowsLiteralValues>false</allowsLiteralValues>
305    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
306  </inputs>
307  <outputs>
308    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
309      <name>return</name>
310      <depth>0</depth>
311      <mimeTypes class="java.util.Collections$SingletonList">
312        <element class="string">'text/plain'</element>
313      </mimeTypes>
314      <granularDepth>0</granularDepth>
315    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
316  </outputs>
317  <wrappedTypeXML>&lt;s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"&gt;&lt;s:complextype optional="false" unbounded="false" typename="getConceptIdsFromTermResponse" name="parameters" qname="{http://ws.apache.org/axis2}getConceptIdsFromTermResponse"&gt;&lt;s:elements&gt;&lt;s:basetype optional="true" unbounded="false" typename="anyType" name="return" qname="{http://ws.apache.org/axis2}&amp;gt;getConceptIdsFromTermResponse&amp;gt;return" /&gt;&lt;/s:elements&gt;&lt;/s:complextype&gt;&lt;/s:extensions&gt;</wrappedTypeXML>
318</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
319  <maxJobs>1</maxJobs>
320</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
321  <backoffFactor>1.0</backoffFactor>
322  <initialDelay>1000</initialDelay>
323  <maxDelay>5000</maxDelay>
324  <maxRetries>0</maxRetries>
325</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="input" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>limit_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
326  <value>10</value>
327</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
328  <maxJobs>1</maxJobs>
329</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
330  <backoffFactor>1.0</backoffFactor>
331  <initialDelay>1000</initialDelay>
332  <maxDelay>5000</maxDelay>
333  <maxRetries>0</maxRetries>
334</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Explain_concept_scores</processor><port>maxNrResults</port></sink><source type="dataflow"><port>maxNrToExplain</port></source></datalink><datalink><sink type="processor"><processor>Explain_concept_scores</processor><port>matchConcept</port></sink><source type="processor"><processor>Match_concept_profiles</processor><port>MatchConceptID</port></source></datalink><datalink><sink type="processor"><processor>Explain_concept_scores</processor><port>queryConceptSet</port></sink><source type="processor"><processor>queryConceptIdsFromTerm</processor><port>return</port></source></datalink><datalink><sink type="processor"><processor>Match_concept_profiles</processor><port>MatchConceptSet</port></sink><source type="processor"><processor>getConceptIdsFromTerm_output</processor><port>return</port></source></datalink><datalink><sink type="processor"><processor>Match_concept_profiles</processor><port>QueryConceptSet</port></sink><source type="processor"><processor>queryConceptIdsFromTerm</processor><port>return</port></source></datalink><datalink><sink type="processor"><processor>Match_concept_profiles</processor><port>Cutoff</port></sink><source type="dataflow"><port>cutOff</port></source></datalink><datalink><sink type="processor"><processor>SplitCSV</processor><port>string</port></sink><source type="dataflow"><port>ProteinList_CSV</port></source></datalink><datalink><sink type="processor"><processor>SplitCSV</processor><port>regex</port></sink><source type="processor"><processor>regex_value</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>getConceptIdsFromTerm</processor><port>parameters</port></sink><source type="processor"><processor>getConceptIdsFromTerm_input</processor><port>output</port></source></datalink><datalink><sink type="processor"><processor>getConceptIdsFromTerm_input</processor><port>term</port></sink><source type="processor"><processor>SplitCSV</processor><port>split</port></source></datalink><datalink><sink type="processor"><processor>getConceptIdsFromTerm_input</processor><port>limit</port></sink><source type="processor"><processor>limit_value</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>getConceptIdsFromTerm_output</processor><port>input</port></sink><source type="processor"><processor>getConceptIdsFromTerm</processor><port>parameters</port></source></datalink><datalink><sink type="processor"><processor>getConceptIdsFromTerm_2</processor><port>parameters</port></sink><source type="processor"><processor>queryTerm</processor><port>output</port></source></datalink><datalink><sink type="processor"><processor>queryTerm</processor><port>term</port></sink><source type="dataflow"><port>queryTerm</port></source></datalink><datalink><sink type="processor"><processor>queryTerm</processor><port>limit</port></sink><source type="processor"><processor>limit_value</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>queryConceptIdsFromTerm</processor><port>input</port></sink><source type="processor"><processor>getConceptIdsFromTerm_2</processor><port>parameters</port></source></datalink><datalink><sink type="dataflow"><port>contributionTable_xml</port></sink><source type="processor"><processor>Explain_concept_scores</processor><port>xml_table</port></source></datalink><datalink><sink type="dataflow"><port>TopMatchingConcepts</port></sink><source type="processor"><processor>Match_concept_profiles</processor><port>MatchResultList</port></source></datalink><datalink><sink type="dataflow"><port>TopContributingConcepts</port></sink><source type="processor"><processor>Explain_concept_scores</processor><port>ConceptName</port></source></datalink><datalink><sink type="dataflow"><port>SummedSimilarity</port></sink><source type="processor"><processor>Match_concept_profiles</processor><port>SummedSimilarityScore</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
335  <annotationAssertions>
336    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
337      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
338        <identification>5c4f140e-14a8-47b9-9775-af75fbd1652a</identification>
339      </annotationBean>
340      <date>2012-04-16 15:25:07.600 CEST</date>
341      <creators />
342      <curationEventList />
343    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
344  </annotationAssertions>
345</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
346  <annotationAssertions>
347    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
348      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
349        <identification>fc7f01a1-0ee9-452f-bbdd-f5420ee6ace7</identification>
350      </annotationBean>
351      <date>2012-04-17 10:47:28.621 CEST</date>
352      <creators />
353      <curationEventList />
354    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
355  </annotationAssertions>
356</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
357  <annotationAssertions>
358    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
359      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
360        <identification>513fb000-c883-4834-8531-95be4fbb258d</identification>
361      </annotationBean>
362      <date>2012-04-16 17:47:16.322 CEST</date>
363      <creators />
364      <curationEventList />
365    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
366  </annotationAssertions>
367</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
368  <annotationAssertions>
369    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
370      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
371        <identification>9cb6f657-6ddc-4209-98b5-9f2ab3586f1f</identification>
372      </annotationBean>
373      <date>2012-04-16 18:03:29.10 CEST</date>
374      <creators />
375      <curationEventList />
376    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
377  </annotationAssertions>
378</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
379  <annotationAssertions>
380    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
381      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.Author">
382        <text>Marco Roos on behalf of the BioSemantics group</text>
383      </annotationBean>
384      <date>2012-04-17 10:32:53.985 CEST</date>
385      <creators />
386      <curationEventList />
387    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
388  </annotationAssertions>
389</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
390  <annotationAssertions>
391    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
392      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
393        <identification>28d4c903-6ba1-4ea3-8acc-34343191d869</identification>
394      </annotationBean>
395      <date>2012-04-16 15:28:03.120 CEST</date>
396      <creators />
397      <curationEventList />
398    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
399  </annotationAssertions>
400</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
401  <annotationAssertions>
402    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
403      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
404        <identification>0ac49425-8699-4745-ae7d-fe01a0274d62</identification>
405      </annotationBean>
406      <date>2012-04-16 15:23:07.226 CEST</date>
407      <creators />
408      <curationEventList />
409    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
410  </annotationAssertions>
411</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
412  <annotationAssertions>
413    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
414      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
415        <identification>5db4cc03-ef86-4b3a-bfa1-f1591b88279e</identification>
416      </annotationBean>
417      <date>2012-04-16 17:10:24.591 CEST</date>
418      <creators />
419      <curationEventList />
420    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
421  </annotationAssertions>
422</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
423  <annotationAssertions>
424    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
425      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
426        <text>This workflow computes the match between a list of proteins and a term of interest 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 protein and the query term.
427
428E.g. (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'.</text>
429      </annotationBean>
430      <date>2012-04-17 10:47:10.173 CEST</date>
431      <creators />
432      <curationEventList />
433    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
434  </annotationAssertions>
435</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
436  <annotationAssertions>
437    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
438      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
439        <identification>4358fb3d-0798-4d38-9b27-2f8fd9943f1c</identification>
440      </annotationBean>
441      <date>2012-04-16 15:33:38.858 CEST</date>
442      <creators />
443      <curationEventList />
444    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
445  </annotationAssertions>
446</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
447  <annotationAssertions>
448    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
449      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
450        <identification>fca39b22-706e-4cfe-a3a9-cab391b7dd78</identification>
451      </annotationBean>
452      <date>2012-04-17 12:46:16.632 CEST</date>
453      <creators />
454      <curationEventList />
455    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
456  </annotationAssertions>
457</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
458  <annotationAssertions>
459    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
460      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
461        <identification>3798ca3e-7639-4b4a-8fa5-5ffe6420d49c</identification>
462      </annotationBean>
463      <date>2012-04-17 10:27:54.811 CEST</date>
464      <creators />
465      <curationEventList />
466    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
467  </annotationAssertions>
468</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
469  <annotationAssertions>
470    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
471      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
472        <identification>6576de34-7532-4585-ad77-9bf5e7441d0d</identification>
473      </annotationBean>
474      <date>2012-04-16 17:13:38.602 CEST</date>
475      <creators />
476      <curationEventList />
477    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
478  </annotationAssertions>
479</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
480  <annotationAssertions>
481    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
482      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
483        <identification>0f302f1f-fb5e-4a98-aab8-f5019742e84a</identification>
484      </annotationBean>
485      <date>2012-04-16 17:04:40.107 CEST</date>
486      <creators />
487      <curationEventList />
488    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
489  </annotationAssertions>
490</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow><dataflow id="9e4c2fcc-6dcc-46d5-9edd-d7841389ef5c" role="nested"><name>Explain_concept_scores</name><inputPorts><port><name>matchConcept</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
491  <annotationAssertions>
492    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
493      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
494        <text>Concept Profile list (by concept identifier). Examples 79822, 25362</text>
495      </annotationBean>
496      <date>2012-04-16 14:57:59.976 CEST</date>
497      <creators />
498      <curationEventList />
499    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
500  </annotationAssertions>
501</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
502  <annotationAssertions>
503    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
504      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
505        <text>79822</text>
506      </annotationBean>
507      <date>2012-04-16 14:58:11.409 CEST</date>
508      <creators />
509      <curationEventList />
510    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
511  </annotationAssertions>
512</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>maxNrResults</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
513  <annotationAssertions>
514    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
515      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
516        <text>Maximum number of concepts to return.</text>
517      </annotationBean>
518      <date>2012-04-16 15:04:21.46 CEST</date>
519      <creators />
520      <curationEventList />
521    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
522  </annotationAssertions>
523</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
524  <annotationAssertions>
525    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
526      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
527        <text>10</text>
528      </annotationBean>
529      <date>2012-04-16 15:04:29.375 CEST</date>
530      <creators />
531      <curationEventList />
532    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
533  </annotationAssertions>
534</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>queryConceptSet</name><depth>1</depth><granularDepth>1</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>ConceptName</name><annotations /></port><port><name>ConceptID</name><annotations /></port><port><name>ConceptContribution</name><annotations /></port><port><name>xml_table</name><annotations /></port></outputPorts><processors><processor><name>return_ConceptContributionTable</name><inputPorts><port><name>input</name><depth>0</depth></port></inputPorts><outputPorts><port><name>ConceptContributionTable</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity</class><inputMap><map from="input" to="input" /></inputMap><outputMap><map from="ConceptContributionTable" to="ConceptContributionTable" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
535  <inputs>
536    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
537      <name>input</name>
538      <depth>0</depth>
539      <mimeTypes class="java.util.Collections$SingletonList">
540        <element class="string">'text/xml'</element>
541      </mimeTypes>
542      <handledReferenceSchemes />
543      <translatedElementType>java.lang.String</translatedElementType>
544      <allowsLiteralValues>false</allowsLiteralValues>
545    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
546  </inputs>
547  <outputs>
548    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
549      <name>ConceptContributionTable</name>
550      <depth>1</depth>
551      <mimeTypes class="java.util.Collections$SingletonList">
552        <element class="string">l('text/xml')</element>
553      </mimeTypes>
554      <granularDepth>1</granularDepth>
555    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
556  </outputs>
557  <wrappedTypeXML>&lt;s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"&gt;&lt;s:arraytype optional="true" unbounded="false" wrapped="true" typename="&amp;gt;conceptContributionsWrapper&amp;gt;ConceptContributionTable" name="ConceptContributionTable" qname="conceptContributionsWrapper&amp;gt;ConceptContributionTable"&gt;&lt;s:elementtype&gt;&lt;s:complextype optional="false" unbounded="false" typename="conceptContribution" name="" qname="{http://services.conceptrecognizer.lumc.nl/}conceptContribution"&gt;&lt;s:elements&gt;&lt;s:basetype optional="true" unbounded="false" typename="string" name="conceptName" qname="conceptContribution&amp;gt;conceptName" /&gt;&lt;s:basetype optional="true" unbounded="false" typename="double" name="contribution" qname="conceptContribution&amp;gt;contribution" /&gt;&lt;s:basetype optional="true" unbounded="false" typename="int" name="conceptId" qname="conceptContribution&amp;gt;conceptId" /&gt;&lt;/s:elements&gt;&lt;/s:complextype&gt;&lt;/s:elementtype&gt;&lt;/s:arraytype&gt;&lt;/s:extensions&gt;</wrappedTypeXML>
558</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
559  <maxJobs>1</maxJobs>
560</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
561  <backoffFactor>1.0</backoffFactor>
562  <initialDelay>1000</initialDelay>
563  <maxDelay>5000</maxDelay>
564  <maxRetries>0</maxRetries>
565</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="input" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>ConceptContributionTable_ConceptContributionTable</name><inputPorts><port><name>input</name><depth>0</depth></port></inputPorts><outputPorts><port><name>conceptId</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>contribution</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>conceptName</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity</class><inputMap><map from="input" to="input" /></inputMap><outputMap><map from="conceptId" to="conceptId" /><map from="contribution" to="contribution" /><map from="conceptName" to="conceptName" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
566  <inputs>
567    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
568      <name>input</name>
569      <depth>0</depth>
570      <mimeTypes class="java.util.Collections$SingletonList">
571        <element class="string">'text/xml'</element>
572      </mimeTypes>
573      <handledReferenceSchemes />
574      <translatedElementType>java.lang.String</translatedElementType>
575      <allowsLiteralValues>false</allowsLiteralValues>
576    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
577  </inputs>
578  <outputs>
579    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
580      <name>conceptName</name>
581      <depth>0</depth>
582      <mimeTypes class="java.util.Collections$SingletonList">
583        <element class="string">'text/plain'</element>
584      </mimeTypes>
585      <granularDepth>0</granularDepth>
586    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
587    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
588      <name>contribution</name>
589      <depth>0</depth>
590      <mimeTypes class="java.util.Collections$SingletonList">
591        <element class="string">'text/plain'</element>
592      </mimeTypes>
593      <granularDepth>0</granularDepth>
594    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
595    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
596      <name>conceptId</name>
597      <depth>0</depth>
598      <mimeTypes class="java.util.Collections$SingletonList">
599        <element class="string">'text/plain'</element>
600      </mimeTypes>
601      <granularDepth>0</granularDepth>
602    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
603  </outputs>
604  <wrappedTypeXML>&lt;s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"&gt;&lt;s:complextype optional="false" unbounded="false" typename="conceptContribution" name="" qname="{http://services.conceptrecognizer.lumc.nl/}conceptContribution"&gt;&lt;s:elements&gt;&lt;s:basetype optional="true" unbounded="false" typename="string" name="conceptName" qname="conceptContribution&amp;gt;conceptName" /&gt;&lt;s:basetype optional="true" unbounded="false" typename="double" name="contribution" qname="conceptContribution&amp;gt;contribution" /&gt;&lt;s:basetype optional="true" unbounded="false" typename="int" name="conceptId" qname="conceptContribution&amp;gt;conceptId" /&gt;&lt;/s:elements&gt;&lt;/s:complextype&gt;&lt;/s:extensions&gt;</wrappedTypeXML>
605</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
606  <maxJobs>1</maxJobs>
607</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
608  <backoffFactor>1.0</backoffFactor>
609  <initialDelay>1000</initialDelay>
610  <maxDelay>5000</maxDelay>
611  <maxRetries>0</maxRetries>
612</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="input" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>explainScores</name><inputPorts><port><name>parameters</name><depth>0</depth></port></inputPorts><outputPorts><port><name>parameters</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="parameters" to="parameters" /></inputMap><outputMap><map from="parameters" to="parameters" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
613  <wsdl>http://ws.biosemantics.org/ConceptRecognizerService?wsdl</wsdl>
614  <operation>explainScores</operation>
615</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
616  <maxJobs>1</maxJobs>
617</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
618  <backoffFactor>1.0</backoffFactor>
619  <initialDelay>1000</initialDelay>
620  <maxDelay>5000</maxDelay>
621  <maxRetries>0</maxRetries>
622</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="parameters" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>explainScores_input</name><inputPorts><port><name>cutoffValue</name><depth>0</depth></port><port><name>conceptCUIs</name><depth>1</depth></port></inputPorts><outputPorts><port><name>output</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity</class><inputMap><map from="cutoffValue" to="cutoffValue" /><map from="conceptCUIs" to="conceptCUIs" /></inputMap><outputMap><map from="output" to="output" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
623  <inputs>
624    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
625      <name>cutoffValue</name>
626      <depth>0</depth>
627      <mimeTypes class="java.util.Collections$SingletonList">
628        <element class="string">'text/plain'</element>
629      </mimeTypes>
630      <allowsLiteralValues>false</allowsLiteralValues>
631    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
632    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
633      <name>conceptCUIs</name>
634      <depth>1</depth>
635      <mimeTypes class="java.util.Collections$SingletonList">
636        <element class="string">l('text/plain')</element>
637      </mimeTypes>
638      <allowsLiteralValues>false</allowsLiteralValues>
639    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
640  </inputs>
641  <outputs>
642    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
643      <name>output</name>
644      <depth>0</depth>
645      <mimeTypes class="java.util.Collections$SingletonList">
646        <element class="string">'text/xml'</element>
647      </mimeTypes>
648      <granularDepth>0</granularDepth>
649    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
650  </outputs>
651  <wrappedTypeXML>&lt;s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"&gt;&lt;s:complextype optional="false" unbounded="false" typename="explainScores" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}explainScores"&gt;&lt;s:elements&gt;&lt;s:basetype optional="false" unbounded="false" typename="int" name="cutoffValue" qname="explainScores&amp;gt;cutoffValue" /&gt;&lt;s:arraytype optional="true" unbounded="true" wrapped="false" typename="int" name="conceptCUIs" qname="explainScores&amp;gt;conceptCUIs"&gt;&lt;s:elementtype&gt;&lt;s:basetype optional="false" unbounded="false" typename="int" name="" qname="{http://www.w3.org/2001/XMLSchema}int" /&gt;&lt;/s:elementtype&gt;&lt;/s:arraytype&gt;&lt;/s:elements&gt;&lt;/s:complextype&gt;&lt;/s:extensions&gt;</wrappedTypeXML>
652</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
653  <maxJobs>1</maxJobs>
654</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
655  <backoffFactor>1.0</backoffFactor>
656  <initialDelay>1000</initialDelay>
657  <maxDelay>5000</maxDelay>
658  <maxRetries>0</maxRetries>
659</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="cutoffValue" depth="0" /><port name="conceptCUIs" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>explainScores_output</name><inputPorts><port><name>input</name><depth>0</depth></port></inputPorts><outputPorts><port><name>return</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity</class><inputMap><map from="input" to="input" /></inputMap><outputMap><map from="return" to="return" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
660  <inputs>
661    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
662      <name>input</name>
663      <depth>0</depth>
664      <mimeTypes class="java.util.Collections$SingletonList">
665        <element class="string">'text/xml'</element>
666      </mimeTypes>
667      <handledReferenceSchemes />
668      <translatedElementType>java.lang.String</translatedElementType>
669      <allowsLiteralValues>false</allowsLiteralValues>
670    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
671  </inputs>
672  <outputs>
673    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
674      <name>return</name>
675      <depth>0</depth>
676      <mimeTypes class="java.util.Collections$SingletonList">
677        <element class="string">'text/xml'</element>
678      </mimeTypes>
679      <granularDepth>0</granularDepth>
680    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
681  </outputs>
682  <wrappedTypeXML>&lt;s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"&gt;&lt;s:complextype optional="false" unbounded="false" typename="explainScoresResponse" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}explainScoresResponse"&gt;&lt;s:elements&gt;&lt;s:complextype optional="true" unbounded="false" typename="conceptContributionsWrapper" name="return" qname="explainScoresResponse&amp;gt;return"&gt;&lt;s:elements&gt;&lt;s:arraytype optional="true" unbounded="false" wrapped="true" typename="&amp;gt;conceptContributionsWrapper&amp;gt;ConceptContributionTable" name="ConceptContributionTable" qname="conceptContributionsWrapper&amp;gt;ConceptContributionTable"&gt;&lt;s:elementtype&gt;&lt;s:complextype optional="false" unbounded="false" typename="conceptContribution" name="" qname="{http://services.conceptrecognizer.lumc.nl/}conceptContribution"&gt;&lt;s:elements&gt;&lt;s:basetype optional="true" unbounded="false" typename="string" name="conceptName" qname="conceptContribution&amp;gt;conceptName" /&gt;&lt;s:basetype optional="true" unbounded="false" typename="double" name="contribution" qname="conceptContribution&amp;gt;contribution" /&gt;&lt;s:basetype optional="true" unbounded="false" typename="int" name="conceptId" qname="conceptContribution&amp;gt;conceptId" /&gt;&lt;/s:elements&gt;&lt;/s:complextype&gt;&lt;/s:elementtype&gt;&lt;/s:arraytype&gt;&lt;/s:elements&gt;&lt;/s:complextype&gt;&lt;/s:elements&gt;&lt;/s:complextype&gt;&lt;/s:extensions&gt;</wrappedTypeXML>
683</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
684  <maxJobs>1</maxJobs>
685</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
686  <backoffFactor>1.0</backoffFactor>
687  <initialDelay>1000</initialDelay>
688  <maxDelay>5000</maxDelay>
689  <maxRetries>0</maxRetries>
690</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="input" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>explainScores_return</name><inputPorts><port><name>input</name><depth>0</depth></port></inputPorts><outputPorts><port><name>ConceptContributionTable</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity</class><inputMap><map from="input" to="input" /></inputMap><outputMap><map from="ConceptContributionTable" to="ConceptContributionTable" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
691  <inputs>
692    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
693      <name>input</name>
694      <depth>0</depth>
695      <mimeTypes class="java.util.Collections$SingletonList">
696        <element class="string">'text/xml'</element>
697      </mimeTypes>
698      <handledReferenceSchemes />
699      <translatedElementType>java.lang.String</translatedElementType>
700      <allowsLiteralValues>false</allowsLiteralValues>
701    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
702  </inputs>
703  <outputs>
704    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
705      <name>ConceptContributionTable</name>
706      <depth>0</depth>
707      <mimeTypes class="java.util.Collections$SingletonList">
708        <element class="string">'text/xml'</element>
709      </mimeTypes>
710      <granularDepth>0</granularDepth>
711    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
712  </outputs>
713  <wrappedTypeXML>&lt;s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"&gt;&lt;s:complextype optional="true" unbounded="false" typename="conceptContributionsWrapper" name="return" qname="explainScoresResponse&amp;gt;return"&gt;&lt;s:elements&gt;&lt;s:arraytype optional="true" unbounded="false" wrapped="true" typename="&amp;gt;conceptContributionsWrapper&amp;gt;ConceptContributionTable" name="ConceptContributionTable" qname="conceptContributionsWrapper&amp;gt;ConceptContributionTable"&gt;&lt;s:elementtype&gt;&lt;s:complextype optional="false" unbounded="false" typename="conceptContribution" name="" qname="{http://services.conceptrecognizer.lumc.nl/}conceptContribution"&gt;&lt;s:elements&gt;&lt;s:basetype optional="true" unbounded="false" typename="string" name="conceptName" qname="conceptContribution&amp;gt;conceptName" /&gt;&lt;s:basetype optional="true" unbounded="false" typename="double" name="contribution" qname="conceptContribution&amp;gt;contribution" /&gt;&lt;s:basetype optional="true" unbounded="false" typename="int" name="conceptId" qname="conceptContribution&amp;gt;conceptId" /&gt;&lt;/s:elements&gt;&lt;/s:complextype&gt;&lt;/s:elementtype&gt;&lt;/s:arraytype&gt;&lt;/s:elements&gt;&lt;/s:complextype&gt;&lt;/s:extensions&gt;</wrappedTypeXML>
714</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
715  <maxJobs>1</maxJobs>
716</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
717  <backoffFactor>1.0</backoffFactor>
718  <initialDelay>1000</initialDelay>
719  <maxDelay>5000</maxDelay>
720  <maxRetries>0</maxRetries>
721</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="input" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Beanshell</name><inputPorts><port><name>item</name><depth>0</depth></port><port><name>inputList</name><depth>1</depth></port></inputPorts><outputPorts><port><name>outputList</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="item" to="item" /><map from="inputList" to="inputList" /></inputMap><outputMap><map from="outputList" to="outputList" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
722  <inputs>
723    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
724      <name>inputList</name>
725      <depth>1</depth>
726      <mimeTypes>
727        <string>text/plain</string>
728      </mimeTypes>
729      <handledReferenceSchemes />
730      <translatedElementType>java.lang.String</translatedElementType>
731      <allowsLiteralValues>true</allowsLiteralValues>
732    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
733    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
734      <name>item</name>
735      <depth>0</depth>
736      <mimeTypes>
737        <string>text/plain</string>
738      </mimeTypes>
739      <handledReferenceSchemes />
740      <translatedElementType>java.lang.String</translatedElementType>
741      <allowsLiteralValues>true</allowsLiteralValues>
742    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
743  </inputs>
744  <outputs>
745    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
746      <name>outputList</name>
747      <depth>1</depth>
748      <mimeTypes />
749      <granularDepth>1</granularDepth>
750    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
751  </outputs>
752  <classLoaderSharing>workflow</classLoaderSharing>
753  <localDependencies />
754  <artifactDependencies />
755  <script>ArrayList tmp = new ArrayList(inputList);
756
757tmp.add(item);
758
759outputList = tmp;</script>
760  <dependencies />
761</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
762  <maxJobs>1</maxJobs>
763</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
764  <backoffFactor>1.0</backoffFactor>
765  <initialDelay>1000</initialDelay>
766  <maxDelay>5000</maxDelay>
767  <maxRetries>0</maxRetries>
768</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="item" depth="0" /><port name="inputList" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>return_ConceptContributionTable</processor><port>input</port></sink><source type="processor"><processor>explainScores_return</processor><port>ConceptContributionTable</port></source></datalink><datalink><sink type="processor"><processor>ConceptContributionTable_ConceptContributionTable</processor><port>input</port></sink><source type="processor"><processor>return_ConceptContributionTable</processor><port>ConceptContributionTable</port></source></datalink><datalink><sink type="processor"><processor>explainScores</processor><port>parameters</port></sink><source type="processor"><processor>explainScores_input</processor><port>output</port></source></datalink><datalink><sink type="processor"><processor>explainScores_input</processor><port>cutoffValue</port></sink><source type="dataflow"><port>maxNrResults</port></source></datalink><datalink><sink type="processor"><processor>explainScores_input</processor><port>conceptCUIs</port></sink><source type="processor"><processor>Beanshell</processor><port>outputList</port></source></datalink><datalink><sink type="processor"><processor>explainScores_output</processor><port>input</port></sink><source type="processor"><processor>explainScores</processor><port>parameters</port></source></datalink><datalink><sink type="processor"><processor>explainScores_return</processor><port>input</port></sink><source type="processor"><processor>explainScores_output</processor><port>return</port></source></datalink><datalink><sink type="processor"><processor>Beanshell</processor><port>item</port></sink><source type="dataflow"><port>matchConcept</port></source></datalink><datalink><sink type="processor"><processor>Beanshell</processor><port>inputList</port></sink><source type="dataflow"><port>queryConceptSet</port></source></datalink><datalink><sink type="dataflow"><port>ConceptName</port></sink><source type="processor"><processor>ConceptContributionTable_ConceptContributionTable</processor><port>conceptName</port></source></datalink><datalink><sink type="dataflow"><port>ConceptID</port></sink><source type="processor"><processor>ConceptContributionTable_ConceptContributionTable</processor><port>conceptId</port></source></datalink><datalink><sink type="dataflow"><port>ConceptContribution</port></sink><source type="processor"><processor>ConceptContributionTable_ConceptContributionTable</processor><port>contribution</port></source></datalink><datalink><sink type="dataflow"><port>xml_table</port></sink><source type="processor"><processor>explainScores_return</processor><port>ConceptContributionTable</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
769  <annotationAssertions>
770    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
771      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
772        <identification>bb8d1d77-e3d2-4cee-aee9-3cd4e1bd8547</identification>
773      </annotationBean>
774      <date>2012-01-06 13:38:00.681 CET</date>
775      <creators />
776      <curationEventList />
777    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
778  </annotationAssertions>
779</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
780  <annotationAssertions>
781    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
782      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
783        <identification>fc7ae322-fcac-41c5-b136-0767d52680b0</identification>
784      </annotationBean>
785      <date>2012-03-21 14:53:26.66 CET</date>
786      <creators />
787      <curationEventList />
788    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
789  </annotationAssertions>
790</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
791  <annotationAssertions>
792    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
793      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
794        <identification>541a7a2d-e3e3-490d-885b-52d653a21d11</identification>
795      </annotationBean>
796      <date>2012-02-03 12:42:15.89 CET</date>
797      <creators />
798      <curationEventList />
799    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
800  </annotationAssertions>
801</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
802  <annotationAssertions>
803    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
804      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
805        <identification>8d4a9091-0ba9-468e-9883-7b08e5212cd2</identification>
806      </annotationBean>
807      <date>2012-04-16 15:07:32.864 CEST</date>
808      <creators />
809      <curationEventList />
810    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
811  </annotationAssertions>
812</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
813  <annotationAssertions>
814    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
815      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
816        <identification>89f2da6a-161b-47b1-a048-a65fd35f912c</identification>
817      </annotationBean>
818      <date>2012-01-06 12:47:16.46 CET</date>
819      <creators />
820      <curationEventList />
821    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
822  </annotationAssertions>
823</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
824  <annotationAssertions>
825    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
826      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.Author">
827        <text>Creator: Reinout van Schouwen on behalf of the BIoSemantics Group
828Adaptation by Marco Roos</text>
829      </annotationBean>
830      <date>2012-04-16 14:59:53.250 CEST</date>
831      <creators />
832      <curationEventList />
833    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
834  </annotationAssertions>
835</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
836  <annotationAssertions>
837    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
838      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
839        <identification>2b5167d3-3864-46c1-b761-b66ab721da54</identification>
840      </annotationBean>
841      <date>2012-02-03 14:52:44.748 CET</date>
842      <creators />
843      <curationEventList />
844    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
845  </annotationAssertions>
846</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
847  <annotationAssertions>
848    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
849      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
850        <identification>0faa8a91-3a1c-4e03-b74d-f271e7b96290</identification>
851      </annotationBean>
852      <date>2012-04-16 14:55:56.499 CEST</date>
853      <creators />
854      <curationEventList />
855    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
856  </annotationAssertions>
857</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
858  <annotationAssertions>
859    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
860      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
861        <text>Explain concept scores of concept profiles (enrichment with concept set)</text>
862      </annotationBean>
863      <date>2012-04-16 15:00:51.27 CEST</date>
864      <creators />
865      <curationEventList />
866    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
867  </annotationAssertions>
868</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
869  <annotationAssertions>
870    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
871      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
872        <identification>4bed166d-9815-4a35-a613-869b300b7973</identification>
873      </annotationBean>
874      <date>2012-04-16 15:04:34.678 CEST</date>
875      <creators />
876      <curationEventList />
877    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
878  </annotationAssertions>
879</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
880  <annotationAssertions>
881    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
882      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
883        <identification>13050a9d-bdda-4de5-8bc7-8503457302cd</identification>
884      </annotationBean>
885      <date>2012-04-16 15:02:36.340 CEST</date>
886      <creators />
887      <curationEventList />
888    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
889  </annotationAssertions>
890</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
891  <annotationAssertions>
892    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
893      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
894        <identification>8efd062c-22d8-4fc6-bfe4-ea8f96ba7e2a</identification>
895      </annotationBean>
896      <date>2012-04-16 14:58:21.8 CEST</date>
897      <creators />
898      <curationEventList />
899    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
900  </annotationAssertions>
901</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
902  <annotationAssertions>
903    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
904      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.DescriptiveTitle">
905        <text>Explain concept scores</text>
906      </annotationBean>
907      <date>2012-04-16 15:00:42.27 CEST</date>
908      <creators />
909      <curationEventList />
910    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
911  </annotationAssertions>
912</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
913  <annotationAssertions>
914    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
915      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
916        <identification>9e4c2fcc-6dcc-46d5-9edd-d7841389ef5c</identification>
917      </annotationBean>
918      <date>2012-04-17 10:22:27.551 CEST</date>
919      <creators />
920      <curationEventList />
921    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
922  </annotationAssertions>
923</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
924  <annotationAssertions>
925    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
926      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
927        <identification>7a995f89-0c37-48b9-b0f7-8eca5cd36420</identification>
928      </annotationBean>
929      <date>2012-01-06 12:51:06.790 CET</date>
930      <creators />
931      <curationEventList />
932    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
933  </annotationAssertions>
934</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
935  <annotationAssertions>
936    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
937      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
938        <identification>abaeb048-e186-4c8d-92d4-6b32b22603d8</identification>
939      </annotationBean>
940      <date>2012-04-16 15:01:16.427 CEST</date>
941      <creators />
942      <curationEventList />
943    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
944  </annotationAssertions>
945</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow><dataflow id="dafd97bb-bd4c-4540-b335-d9cfe2d84108" role="nested"><name>Match_concept_profiles</name><inputPorts><port><name>Cutoff</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
946  <annotationAssertions>
947    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
948      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
949        <text>25</text>
950      </annotationBean>
951      <date>2011-09-27 15:18:52.151 CEST</date>
952      <creators />
953      <curationEventList />
954    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
955  </annotationAssertions>
956</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
957  <annotationAssertions>
958    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
959      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
960        <text>The number of resulting matched concepts that will be shown. </text>
961      </annotationBean>
962      <date>2012-04-16 14:36:29.53 CEST</date>
963      <creators />
964      <curationEventList />
965    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
966  </annotationAssertions>
967</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>MatchConceptSet</name><depth>1</depth><granularDepth>1</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
968  <annotationAssertions>
969    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
970      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
971        <text>3088049</text>
972      </annotationBean>
973      <date>2012-04-16 14:38:41.720 CEST</date>
974      <creators />
975      <curationEventList />
976    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
977  </annotationAssertions>
978</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
979  <annotationAssertions>
980    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
981      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
982        <text>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</text>
983      </annotationBean>
984      <date>2012-04-16 14:38:17.919 CEST</date>
985      <creators />
986      <curationEventList />
987    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
988  </annotationAssertions>
989</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>QueryConceptSet</name><depth>1</depth><granularDepth>1</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
990  <annotationAssertions>
991    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
992      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
993        <text>4275360</text>
994      </annotationBean>
995      <date>2012-04-16 14:39:21.505 CEST</date>
996      <creators />
997      <curationEventList />
998    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
999  </annotationAssertions>
1000</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
1001  <annotationAssertions>
1002    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1003      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
1004        <text>The ConceptSet (a list of concept identifiers) to be queried. For example: 4275360</text>
1005      </annotationBean>
1006      <date>2012-04-16 14:39:57.499 CEST</date>
1007      <creators />
1008      <curationEventList />
1009    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1010  </annotationAssertions>
1011</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port></inputPorts><outputPorts><port><name>MatchResultList</name><annotations /></port><port><name>SimilarityScore</name><annotations /></port><port><name>SummedSimilarityScore</name><annotations /></port><port><name>MatchConceptID</name><annotations /></port></outputPorts><processors><processor><name>getSimilarConceptProfiles</name><inputPorts><port><name>parameters</name><depth>0</depth></port></inputPorts><outputPorts><port><name>parameters</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="parameters" to="parameters" /></inputMap><outputMap><map from="parameters" to="parameters" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
1012  <wsdl>http://ws.biosemantics.org/ConceptRecognizerService?wsdl</wsdl>
1013  <operation>getSimilarConceptProfiles</operation>
1014</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
1015  <maxJobs>1</maxJobs>
1016</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
1017  <backoffFactor>1.0</backoffFactor>
1018  <initialDelay>1000</initialDelay>
1019  <maxDelay>5000</maxDelay>
1020  <maxRetries>0</maxRetries>
1021</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="parameters" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>getSimilarConceptProfiles_input</name><inputPorts><port><name>cutoffValue</name><depth>0</depth></port><port><name>queryConceptProfileList</name><depth>1</depth></port><port><name>matchConceptProfileList</name><depth>1</depth></port></inputPorts><outputPorts><port><name>output</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity</class><inputMap><map from="cutoffValue" to="cutoffValue" /><map from="matchConceptProfileList" to="matchConceptProfileList" /><map from="queryConceptProfileList" to="queryConceptProfileList" /></inputMap><outputMap><map from="output" to="output" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
1022  <inputs>
1023    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
1024      <name>cutoffValue</name>
1025      <depth>0</depth>
1026      <mimeTypes class="java.util.Collections$SingletonList">
1027        <element class="string">'text/plain'</element>
1028      </mimeTypes>
1029      <allowsLiteralValues>false</allowsLiteralValues>
1030    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
1031    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
1032      <name>matchConceptProfileList</name>
1033      <depth>1</depth>
1034      <mimeTypes class="java.util.Collections$SingletonList">
1035        <element class="string">l('text/plain')</element>
1036      </mimeTypes>
1037      <allowsLiteralValues>false</allowsLiteralValues>
1038    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
1039    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
1040      <name>queryConceptProfileList</name>
1041      <depth>1</depth>
1042      <mimeTypes class="java.util.Collections$SingletonList">
1043        <element class="string">l('text/plain')</element>
1044      </mimeTypes>
1045      <allowsLiteralValues>false</allowsLiteralValues>
1046    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
1047  </inputs>
1048  <outputs>
1049    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
1050      <name>output</name>
1051      <depth>0</depth>
1052      <mimeTypes class="java.util.Collections$SingletonList">
1053        <element class="string">'text/xml'</element>
1054      </mimeTypes>
1055      <granularDepth>0</granularDepth>
1056    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
1057  </outputs>
1058  <wrappedTypeXML>&lt;s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"&gt;&lt;s:complextype optional="false" unbounded="false" typename="getSimilarConceptProfiles" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}getSimilarConceptProfiles"&gt;&lt;s:elements&gt;&lt;s:basetype optional="false" unbounded="false" typename="int" name="cutoffValue" qname="getSimilarConceptProfiles&amp;gt;cutoffValue" /&gt;&lt;s:arraytype optional="true" unbounded="true" wrapped="false" typename="int" name="matchConceptProfileList" qname="getSimilarConceptProfiles&amp;gt;matchConceptProfileList"&gt;&lt;s:elementtype&gt;&lt;s:basetype optional="false" unbounded="false" typename="int" name="" qname="{http://www.w3.org/2001/XMLSchema}int" /&gt;&lt;/s:elementtype&gt;&lt;/s:arraytype&gt;&lt;s:arraytype optional="true" unbounded="true" wrapped="false" typename="int" name="queryConceptProfileList" qname="getSimilarConceptProfiles&amp;gt;queryConceptProfileList"&gt;&lt;s:elementtype&gt;&lt;s:basetype optional="false" unbounded="false" typename="int" name="" qname="{http://www.w3.org/2001/XMLSchema}int" /&gt;&lt;/s:elementtype&gt;&lt;/s:arraytype&gt;&lt;/s:elements&gt;&lt;/s:complextype&gt;&lt;/s:extensions&gt;</wrappedTypeXML>
1059</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
1060  <maxJobs>1</maxJobs>
1061</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
1062  <backoffFactor>1.0</backoffFactor>
1063  <initialDelay>1000</initialDelay>
1064  <maxDelay>5000</maxDelay>
1065  <maxRetries>0</maxRetries>
1066</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="cutoffValue" depth="0" /><port name="queryConceptProfileList" depth="1" /><port name="matchConceptProfileList" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>getSimilarConceptProfiles_output</name><inputPorts><port><name>input</name><depth>0</depth></port></inputPorts><outputPorts><port><name>MatchingResult</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity</class><inputMap><map from="input" to="input" /></inputMap><outputMap><map from="MatchingResult" to="MatchingResult" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
1067  <inputs>
1068    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
1069      <name>input</name>
1070      <depth>0</depth>
1071      <mimeTypes class="java.util.Collections$SingletonList">
1072        <element class="string">'text/xml'</element>
1073      </mimeTypes>
1074      <handledReferenceSchemes />
1075      <translatedElementType>java.lang.String</translatedElementType>
1076      <allowsLiteralValues>false</allowsLiteralValues>
1077    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
1078  </inputs>
1079  <outputs>
1080    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
1081      <name>MatchingResult</name>
1082      <depth>0</depth>
1083      <mimeTypes class="java.util.Collections$SingletonList">
1084        <element class="string">'text/xml'</element>
1085      </mimeTypes>
1086      <granularDepth>0</granularDepth>
1087    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
1088  </outputs>
1089  <wrappedTypeXML>&lt;s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"&gt;&lt;s:complextype optional="false" unbounded="false" typename="getSimilarConceptProfilesResponse" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}getSimilarConceptProfilesResponse"&gt;&lt;s:elements&gt;&lt;s:complextype optional="true" unbounded="false" typename="matchingResult" name="MatchingResult" qname="getSimilarConceptProfilesResponse&amp;gt;MatchingResult"&gt;&lt;s:elements&gt;&lt;s:arraytype optional="true" unbounded="false" wrapped="true" typename="&amp;gt;matchingResult&amp;gt;MatchConceptProfileList" name="MatchConceptProfileList" qname="matchingResult&amp;gt;MatchConceptProfileList"&gt;&lt;s:elementtype&gt;&lt;s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /&gt;&lt;/s:elementtype&gt;&lt;/s:arraytype&gt;&lt;s:arraytype optional="true" unbounded="false" wrapped="true" typename="similarityScoreLists" name="SimilarityScoreLists" qname="matchingResult&amp;gt;SimilarityScoreLists"&gt;&lt;s:elementtype&gt;&lt;s:arraytype optional="false" unbounded="false" wrapped="true" typename="scoreListImpl" name="ArrayOfdouble" qname="{http://services.conceptrecognizer.lumc.nl/}scoreListImpl"&gt;&lt;s:elementtype&gt;&lt;s:basetype optional="false" unbounded="false" typename="double" name="" qname="{http://www.w3.org/2001/XMLSchema}double" /&gt;&lt;/s:elementtype&gt;&lt;/s:arraytype&gt;&lt;/s:elementtype&gt;&lt;/s:arraytype&gt;&lt;s:arraytype optional="true" unbounded="false" wrapped="true" typename="&amp;gt;matchingResult&amp;gt;SummedSimilarityScoreList" name="SummedSimilarityScoreList" qname="matchingResult&amp;gt;SummedSimilarityScoreList"&gt;&lt;s:elementtype&gt;&lt;s:basetype optional="false" unbounded="false" typename="double" name="" qname="{http://www.w3.org/2001/XMLSchema}double" /&gt;&lt;/s:elementtype&gt;&lt;/s:arraytype&gt;&lt;/s:elements&gt;&lt;/s:complextype&gt;&lt;/s:elements&gt;&lt;/s:complextype&gt;&lt;/s:extensions&gt;</wrappedTypeXML>
1090</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
1091  <maxJobs>1</maxJobs>
1092</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
1093  <backoffFactor>1.0</backoffFactor>
1094  <initialDelay>1000</initialDelay>
1095  <maxDelay>5000</maxDelay>
1096  <maxRetries>0</maxRetries>
1097</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="input" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>getSimilarConceptProfiles_MatchingResult</name><inputPorts><port><name>input</name><depth>0</depth></port></inputPorts><outputPorts><port><name>MatchConceptProfileList</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>SimilarityScoreLists</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>SummedSimilarityScoreList</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity</class><inputMap><map from="input" to="input" /></inputMap><outputMap><map from="MatchConceptProfileList" to="MatchConceptProfileList" /><map from="SimilarityScoreLists" to="SimilarityScoreLists" /><map from="SummedSimilarityScoreList" to="SummedSimilarityScoreList" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
1098  <inputs>
1099    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
1100      <name>input</name>
1101      <depth>0</depth>
1102      <mimeTypes class="java.util.Collections$SingletonList">
1103        <element class="string">'text/xml'</element>
1104      </mimeTypes>
1105      <handledReferenceSchemes />
1106      <translatedElementType>java.lang.String</translatedElementType>
1107      <allowsLiteralValues>false</allowsLiteralValues>
1108    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
1109  </inputs>
1110  <outputs>
1111    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
1112      <name>MatchConceptProfileList</name>
1113      <depth>1</depth>
1114      <mimeTypes class="java.util.Collections$SingletonList">
1115        <element class="string">l('text/plain')</element>
1116      </mimeTypes>
1117      <granularDepth>1</granularDepth>
1118    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
1119    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
1120      <name>SimilarityScoreLists</name>
1121      <depth>0</depth>
1122      <mimeTypes class="java.util.Collections$SingletonList">
1123        <element class="string">'text/xml'</element>
1124      </mimeTypes>
1125      <granularDepth>0</granularDepth>
1126    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
1127    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
1128      <name>SummedSimilarityScoreList</name>
1129      <depth>1</depth>
1130      <mimeTypes class="java.util.Collections$SingletonList">
1131        <element class="string">l('text/plain')</element>
1132      </mimeTypes>
1133      <granularDepth>1</granularDepth>
1134    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
1135  </outputs>
1136  <wrappedTypeXML>&lt;s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"&gt;&lt;s:complextype optional="true" unbounded="false" typename="matchingResult" name="MatchingResult" qname="getSimilarConceptProfilesResponse&amp;gt;MatchingResult"&gt;&lt;s:elements&gt;&lt;s:arraytype optional="true" unbounded="false" wrapped="true" typename="&amp;gt;matchingResult&amp;gt;MatchConceptProfileList" name="MatchConceptProfileList" qname="matchingResult&amp;gt;MatchConceptProfileList"&gt;&lt;s:elementtype&gt;&lt;s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /&gt;&lt;/s:elementtype&gt;&lt;/s:arraytype&gt;&lt;s:arraytype optional="true" unbounded="false" wrapped="true" typename="similarityScoreLists" name="SimilarityScoreLists" qname="matchingResult&amp;gt;SimilarityScoreLists"&gt;&lt;s:elementtype&gt;&lt;s:arraytype optional="false" unbounded="false" wrapped="true" typename="scoreListImpl" name="ArrayOfdouble" qname="{http://services.conceptrecognizer.lumc.nl/}scoreListImpl"&gt;&lt;s:elementtype&gt;&lt;s:basetype optional="false" unbounded="false" typename="double" name="" qname="{http://www.w3.org/2001/XMLSchema}double" /&gt;&lt;/s:elementtype&gt;&lt;/s:arraytype&gt;&lt;/s:elementtype&gt;&lt;/s:arraytype&gt;&lt;s:arraytype optional="true" unbounded="false" wrapped="true" typename="&amp;gt;matchingResult&amp;gt;SummedSimilarityScoreList" name="SummedSimilarityScoreList" qname="matchingResult&amp;gt;SummedSimilarityScoreList"&gt;&lt;s:elementtype&gt;&lt;s:basetype optional="false" unbounded="false" typename="double" name="" qname="{http://www.w3.org/2001/XMLSchema}double" /&gt;&lt;/s:elementtype&gt;&lt;/s:arraytype&gt;&lt;/s:elements&gt;&lt;/s:complextype&gt;&lt;/s:extensions&gt;</wrappedTypeXML>
1137</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
1138  <maxJobs>1</maxJobs>
1139</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
1140  <backoffFactor>1.0</backoffFactor>
1141  <initialDelay>1000</initialDelay>
1142  <maxDelay>5000</maxDelay>
1143  <maxRetries>0</maxRetries>
1144</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="input" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Filter_ConceptID</name><inputPorts><port><name>regex</name><depth>0</depth></port><port><name>group</name><depth>0</depth></port><port><name>stringlist</name><depth>1</depth></port></inputPorts><outputPorts><port><name>filteredlist</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="regex" to="regex" /><map from="stringlist" to="stringlist" /><map from="group" to="group" /></inputMap><outputMap><map from="filteredlist" to="filteredlist" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
1145  <inputs>
1146    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
1147      <name>stringlist</name>
1148      <depth>1</depth>
1149      <mimeTypes>
1150        <string>l('text/plain')</string>
1151      </mimeTypes>
1152      <handledReferenceSchemes />
1153      <translatedElementType>java.lang.String</translatedElementType>
1154      <allowsLiteralValues>true</allowsLiteralValues>
1155    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
1156    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
1157      <name>regex</name>
1158      <depth>0</depth>
1159      <mimeTypes>
1160        <string>'text/plain'</string>
1161      </mimeTypes>
1162      <handledReferenceSchemes />
1163      <translatedElementType>java.lang.String</translatedElementType>
1164      <allowsLiteralValues>true</allowsLiteralValues>
1165    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
1166    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
1167      <name>group</name>
1168      <depth>0</depth>
1169      <mimeTypes>
1170        <string>'text/plain'</string>
1171      </mimeTypes>
1172      <handledReferenceSchemes />
1173      <translatedElementType>java.lang.String</translatedElementType>
1174      <allowsLiteralValues>true</allowsLiteralValues>
1175    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
1176  </inputs>
1177  <outputs>
1178    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
1179      <name>filteredlist</name>
1180      <depth>1</depth>
1181      <mimeTypes>
1182        <string>l('text/plain')</string>
1183      </mimeTypes>
1184      <granularDepth>1</granularDepth>
1185    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
1186  </outputs>
1187  <classLoaderSharing>workflow</classLoaderSharing>
1188  <localDependencies />
1189  <artifactDependencies />
1190  <script>import java.util.regex.*;
1191
1192filteredlist = new ArrayList();
1193Pattern thePat = Pattern.compile(regex);
1194int theGroup = Integer.parseInt(group);
1195
1196for (Iterator i = stringlist.iterator(); i.hasNext();) {
1197        String item = (String) i.next();
1198        Matcher matcher = thePat.matcher(item);
1199
1200        if (matcher.find()) {
1201                filteredlist.add(matcher.group(theGroup));
1202        }
1203}
1204</script>
1205  <dependencies />
1206  <localworkerName>org.embl.ebi.escience.scuflworkers.java.RegularExpressionStringList</localworkerName>
1207</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
1208  <maxJobs>1</maxJobs>
1209</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
1210  <backoffFactor>1.0</backoffFactor>
1211  <initialDelay>1000</initialDelay>
1212  <maxDelay>5000</maxDelay>
1213  <maxRetries>0</maxRetries>
1214</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="regex" depth="0" /><port name="group" depth="0" /><port name="stringlist" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>regex_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
1215  <value>&lt;http://rdf.biosemantics.org/owl/concept#(.+)/&gt;</value>
1216</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
1217  <maxJobs>1</maxJobs>
1218</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
1219  <backoffFactor>1.0</backoffFactor>
1220  <initialDelay>1000</initialDelay>
1221  <maxDelay>5000</maxDelay>
1222  <maxRetries>0</maxRetries>
1223</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>group_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
1224  <value>1</value>
1225</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
1226  <maxJobs>1</maxJobs>
1227</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
1228  <backoffFactor>1.0</backoffFactor>
1229  <initialDelay>1000</initialDelay>
1230  <maxDelay>5000</maxDelay>
1231  <maxRetries>0</maxRetries>
1232</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>getSimilarConceptProfiles</processor><port>parameters</port></sink><source type="processor"><processor>getSimilarConceptProfiles_input</processor><port>output</port></source></datalink><datalink><sink type="processor"><processor>getSimilarConceptProfiles_input</processor><port>cutoffValue</port></sink><source type="dataflow"><port>Cutoff</port></source></datalink><datalink><sink type="processor"><processor>getSimilarConceptProfiles_input</processor><port>queryConceptProfileList</port></sink><source type="dataflow"><port>QueryConceptSet</port></source></datalink><datalink><sink type="processor"><processor>getSimilarConceptProfiles_input</processor><port>matchConceptProfileList</port></sink><source type="dataflow"><port>MatchConceptSet</port></source></datalink><datalink><sink type="processor"><processor>getSimilarConceptProfiles_output</processor><port>input</port></sink><source type="processor"><processor>getSimilarConceptProfiles</processor><port>parameters</port></source></datalink><datalink><sink type="processor"><processor>getSimilarConceptProfiles_MatchingResult</processor><port>input</port></sink><source type="processor"><processor>getSimilarConceptProfiles_output</processor><port>MatchingResult</port></source></datalink><datalink><sink type="processor"><processor>Filter_ConceptID</processor><port>regex</port></sink><source type="processor"><processor>regex_value</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Filter_ConceptID</processor><port>group</port></sink><source type="processor"><processor>group_value</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Filter_ConceptID</processor><port>stringlist</port></sink><source type="processor"><processor>getSimilarConceptProfiles_MatchingResult</processor><port>MatchConceptProfileList</port></source></datalink><datalink><sink type="dataflow"><port>MatchResultList</port></sink><source type="processor"><processor>getSimilarConceptProfiles_MatchingResult</processor><port>MatchConceptProfileList</port></source></datalink><datalink><sink type="dataflow"><port>SimilarityScore</port></sink><source type="processor"><processor>getSimilarConceptProfiles_MatchingResult</processor><port>SimilarityScoreLists</port></source></datalink><datalink><sink type="dataflow"><port>SummedSimilarityScore</port></sink><source type="processor"><processor>getSimilarConceptProfiles_MatchingResult</processor><port>SummedSimilarityScoreList</port></source></datalink><datalink><sink type="dataflow"><port>MatchConceptID</port></sink><source type="processor"><processor>Filter_ConceptID</processor><port>filteredlist</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
1233  <annotationAssertions>
1234    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1235      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
1236        <identification>0dcad6f0-b77c-4d5d-ae1b-893a7b2436a6</identification>
1237      </annotationBean>
1238      <date>2011-09-28 14:12:42.334 CEST</date>
1239      <creators />
1240      <curationEventList />
1241    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1242  </annotationAssertions>
1243</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
1244  <annotationAssertions>
1245    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1246      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
1247        <identification>487ca7a4-63fa-45f9-baab-8f9a053ca9d0</identification>
1248      </annotationBean>
1249      <date>2012-04-16 14:50:38.225 CEST</date>
1250      <creators />
1251      <curationEventList />
1252    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1253  </annotationAssertions>
1254</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
1255  <annotationAssertions>
1256    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1257      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.DescriptiveTitle">
1258        <text>Match concept profiles</text>
1259      </annotationBean>
1260      <date>2011-09-28 13:31:19.752 CEST</date>
1261      <creators />
1262      <curationEventList />
1263    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1264  </annotationAssertions>
1265</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
1266  <annotationAssertions>
1267    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1268      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
1269        <text>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.</text>
1270      </annotationBean>
1271      <date>2012-04-16 14:50:01.68 CEST</date>
1272      <creators />
1273      <curationEventList />
1274    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1275  </annotationAssertions>
1276</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
1277  <annotationAssertions>
1278    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1279      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
1280        <identification>7986f41c-7556-45d9-bcb3-f557b69f3acc</identification>
1281      </annotationBean>
1282      <date>2012-04-15 22:28:43.911 CEST</date>
1283      <creators />
1284      <curationEventList />
1285    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1286  </annotationAssertions>
1287</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
1288  <annotationAssertions>
1289    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1290      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
1291        <identification>1b7115f7-7832-4081-88df-c6ce4775238f</identification>
1292      </annotationBean>
1293      <date>2011-09-28 13:35:31.328 CEST</date>
1294      <creators />
1295      <curationEventList />
1296    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1297  </annotationAssertions>
1298</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
1299  <annotationAssertions>
1300    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1301      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
1302        <identification>ae37940d-e39c-43c2-80bf-512e60710201</identification>
1303      </annotationBean>
1304      <date>2012-04-16 14:45:48.511 CEST</date>
1305      <creators />
1306      <curationEventList />
1307    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1308  </annotationAssertions>
1309</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
1310  <annotationAssertions>
1311    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1312      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.Author">
1313        <text>Kristina Hettne</text>
1314      </annotationBean>
1315      <date>2011-09-28 13:30:59.360 CEST</date>
1316      <creators />
1317      <curationEventList />
1318    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1319  </annotationAssertions>
1320</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
1321  <annotationAssertions>
1322    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1323      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
1324        <identification>4d330136-ca78-4fa0-ad95-0d34b85f8a76</identification>
1325      </annotationBean>
1326      <date>2011-09-20 17:56:44.26 CEST</date>
1327      <creators />
1328      <curationEventList />
1329    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1330  </annotationAssertions>
1331</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
1332  <annotationAssertions>
1333    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1334      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
1335        <identification>15145a87-30e2-4e04-97a9-10572ff64aae</identification>
1336      </annotationBean>
1337      <date>2011-09-28 13:37:06.330 CEST</date>
1338      <creators />
1339      <curationEventList />
1340    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1341  </annotationAssertions>
1342</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
1343  <annotationAssertions>
1344    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1345      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
1346        <identification>dafd97bb-bd4c-4540-b335-d9cfe2d84108</identification>
1347      </annotationBean>
1348      <date>2012-04-16 17:04:13.913 CEST</date>
1349      <creators />
1350      <curationEventList />
1351    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1352  </annotationAssertions>
1353</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
1354  <annotationAssertions>
1355    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1356      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
1357        <identification>09430282-326d-4c5b-85a8-28ddfc97753e</identification>
1358      </annotationBean>
1359      <date>2011-09-27 17:31:47.87 CEST</date>
1360      <creators />
1361      <curationEventList />
1362    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1363  </annotationAssertions>
1364</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
1365  <annotationAssertions>
1366    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1367      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
1368        <identification>abeb3495-f850-47e4-bc90-018b36584092</identification>
1369      </annotationBean>
1370      <date>2011-09-28 14:24:29.380 CEST</date>
1371      <creators />
1372      <curationEventList />
1373    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1374  </annotationAssertions>
1375</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
1376  <annotationAssertions>
1377    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1378      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
1379        <identification>c55d2bf1-a3b9-46b1-a486-97b4b03eca20</identification>
1380      </annotationBean>
1381      <date>2012-04-16 17:03:34.648 CEST</date>
1382      <creators />
1383      <curationEventList />
1384    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1385  </annotationAssertions>
1386</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
1387  <annotationAssertions>
1388    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1389      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
1390        <identification>9a1764af-8145-4c13-a849-38a031e6f2dd</identification>
1391      </annotationBean>
1392      <date>2011-09-28 14:26:45.132 CEST</date>
1393      <creators />
1394      <curationEventList />
1395    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1396  </annotationAssertions>
1397</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
1398  <annotationAssertions>
1399    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1400      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
1401        <identification>46181b16-64e9-40aa-8dde-b32a9478fe1d</identification>
1402      </annotationBean>
1403      <date>2011-09-27 17:29:17.819 CEST</date>
1404      <creators />
1405      <curationEventList />
1406    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1407  </annotationAssertions>
1408</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
1409  <annotationAssertions>
1410    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1411      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
1412        <identification>1d5bb33c-d18f-4d9c-9ead-487ab5271b7a</identification>
1413      </annotationBean>
1414      <date>2011-09-27 17:37:33.997 CEST</date>
1415      <creators />
1416      <curationEventList />
1417    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1418  </annotationAssertions>
1419</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
1420  <annotationAssertions>
1421    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1422      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
1423        <identification>ffd57175-7b65-4edb-9086-42bad4170b46</identification>
1424      </annotationBean>
1425      <date>2011-09-27 15:41:33.82 CEST</date>
1426      <creators />
1427      <curationEventList />
1428    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1429  </annotationAssertions>
1430</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
1431  <annotationAssertions>
1432    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1433      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
1434        <identification>da482794-4042-408d-adc4-c035dcb831ab</identification>
1435      </annotationBean>
1436      <date>2012-04-16 14:41:12.260 CEST</date>
1437      <creators />
1438      <curationEventList />
1439    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1440  </annotationAssertions>
1441</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
1442  <annotationAssertions>
1443    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1444      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
1445        <identification>fafb8d94-026f-4044-b3ce-866fc199229b</identification>
1446      </annotationBean>
1447      <date>2011-09-28 14:06:54.60 CEST</date>
1448      <creators />
1449      <curationEventList />
1450    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1451  </annotationAssertions>
1452</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
1453  <annotationAssertions>
1454    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1455      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
1456        <identification>ea38018e-ee90-4ccb-ab8e-78eeec907cad</identification>
1457      </annotationBean>
1458      <date>2011-09-28 14:02:39.57 CEST</date>
1459      <creators />
1460      <curationEventList />
1461    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
1462  </annotationAssertions>
1463</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
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