Annotate_a_gene_listEntrez_gene_DB_ID00The ID for the EntrezGene database (Erasmus MC ontology format).2013-02-06 19:25:33.892 UTCEG2013-02-06 11:12:23.506 UTCEntrez_gene_IDs111281
28959
7805
54829
6122
653881
401331
10156
7846
392437
2512
10457
8406
483
7139
64231
6696
6277
5641
3126
3123
302
303
305
11031
929
972
7431
3125
158471
6275
3122
9168
7076
653214
439953
5478
6281
4267
6284
1601
84790
1278
399942
10376
1192
710
4626
4621
4635
26509
4636
6678
10763
301
645715
1915
158078
441032
7351
3115
1462
3108
6303
642741
718
100133511
653879
1134
2202
1756
2014
1634
9332
4069
84617
51155
10577
7305
23643
4060
960
6387
3113
715
8635
1290
3428
414308
712
3150
5118
1277
716
4256
7412
1436
5997
70
4608
8673
3075
1293
10234
729659
62822013-02-06 11:32:07.703 UTCGenes to be annotated (Entrez gene format, see http://www.ncbi.nlm.nih.gov/gene)2013-02-06 19:25:08.98 UTCDisease_or_syndrome_concept_set00822013-02-06 11:12:27.823 UTCID of the predefined concept set to match with. These IDs can be retrieved by running the List Concept Sets workflow (http://www.myexperiment.org/workflows/2999). The example ID corresponds to the concept set "Disease or Syndrome".2013-02-06 19:26:22.730 UTCMatch_concept_cutoff0052013-02-06 13:45:42.907 UTCMax number of concepts to return from the concept profile matching procedure.2013-02-06 19:24:05.487 UTCExplained_concepts_cutoff00Max number of explanatory concepts to return for a concept profile match.2013-02-06 19:40:41.833 UTC102013-02-06 13:59:45.824 UTCMatched_disease_namesmuscular dystrophy, duchenne
hereditary angioneurotic edema
osteogenesis imperfecta
LGMD2B
Rieger syndrome
2013-02-06 19:48:47.811 UTCNames for the concepts from the concept profile match.2013-02-06 19:48:22.482 UTCSummed_Similarity_scoreConcept match similarity score from the matching procedure.2013-02-06 19:46:50.179 UTC0.00885673714427425
0.007450532171402273
0.00504372819304191
0.004096281111489342
0.0038713032622080803
2013-02-06 19:47:05.505 UTCExplained_concept_nameExample list to large to list here, below a subset.
muscular dystrophy2013-02-06 19:52:05.875 UTCThe concept names of the explanatory concepts.2013-02-06 19:51:33.921 UTCExplained_concept_IDExample list to large to list here, below a subset.
http://rdf.biosemantics.org/owl/concept#268502013-02-06 19:52:25.262 UTCThe concept IDs of the explanatory concepts.2013-02-06 19:52:37.886 UTCMatch_concept_IDIDs for the concepts from the concept profile match.2013-02-06 19:49:05.859 UTChttp://rdf.biosemantics.org/owl/concept#13264
http://rdf.biosemantics.org/owl/concept#19243
http://rdf.biosemantics.org/owl/concept#29434
http://rdf.biosemantics.org/owl/concept#1850889
http://rdf.biosemantics.org/owl/concept#265341
2013-02-06 19:49:21.658 UTCQuery_concept_IDExample list to large to list here, below a subset.
http://rdf.biosemantics.org/owl/concept#30915262013-02-06 19:51:07.660 UTCIDs for the concepts from the concept profile query.2013-02-06 19:49:43.174 UTCMatch_concept_profilesCutoff0Match_concept_set0Query_concept_ID0Similarity_score11Match_concept_ID11Query_concept_ID11Purpose of component in workflow:
The purpose of this component (nested workflow) in this workflow is to match the concept profiles of genes to the profiles of disease concepts (from the Disease or Syndrome branch).
Results:
The results of this component are diseases associated with genes, ranked in the order of the match score between the input concepts. The results suggest which diseases are associated with the difference in gene expression in the underlying experiment.2013-02-06 19:37:58.222 UTCnet.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeDatabaseID_to_ConceptIDDatabaseID0IDvalue0Concept_IDs00Purpose of component in workflow:
The purpose of this component (nested workflow) here is to map Entrez gene identifiers (the external database identifiers) to the concept identifier used in the Erasmus MC ontology, developed by the BioSemantics Group in Rotterdam. The ontology can be seen as a concept database compiled from various common thesauri and ontologies.2013-02-06 19:32:51.153 UTCnet.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSplit_string_into_string_list_by_regular_expressionregex0string0split11This local service prepares the list of genes for fast processing: make comma-separated list.2013-02-06 19:43:15.296 UTCnet.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivitystring0'text/plain'java.lang.Stringtrueregex0'text/plain'java.lang.Stringtruesplit1l('text/plain')1workfloworg.embl.ebi.escience.scuflworkers.java.SplitByRegexnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeText_constantvalue00The constant that is used by the local service, in this case ",".2013-02-06 19:44:09.439 UTCnet.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity\nnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGet_concept_nameConcept_ID0Concept_name00Purpose of component in workflow:
To retrieve the name of the concept from the ontology.2013-02-06 19:38:43.270 UTCnet.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeMerge_String_List_to_a_Stringseperator0stringlist1concatenated00This local service prepares the list of concepts for fast processing: make comma-separated list.2013-02-06 19:43:30.163 UTCnet.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivitystringlist1l('text/plain')java.lang.Stringtrueseperator0'text/plain'java.lang.Stringtrueconcatenated0'text/plain'0workfloworg.embl.ebi.escience.scuflworkers.java.StringListMergenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeText_constant_2value00The constant that is used by the local service, in this case ",".2013-02-06 19:44:22.819 UTCnet.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity,net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExplain_concept_scoresC_ConceptID0cutoff0A_ConceptID0B_ConceptName11B_ConceptID11Purpose of component in workflow:
This component retieves the concepts contributing most to the match perfomed in the Match_concept_profiles component.2013-02-06 19:38:26.626 UTCnet.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeMatch_concept_profilesCutoffMatch_concept_profilesMatch_concept_setMatch_concept_profilesQuery_concept_IDDatabaseID_to_ConceptIDDatabaseIDDatabaseID_to_ConceptIDIDvalueSplit_string_into_string_list_by_regular_expressionregexSplit_string_into_string_list_by_regular_expressionstringGet_concept_nameConcept_IDMerge_String_List_to_a_StringseperatorMerge_String_List_to_a_StringstringlistExplain_concept_scoresC_ConceptIDExplain_concept_scorescutoffExplain_concept_scoresA_ConceptIDMatched_disease_namesSummed_Similarity_scoreExplained_concept_nameExplained_concept_IDMatch_concept_IDQuery_concept_ID7df07095-ba57-402a-bc57-b062f18c03822013-02-06 11:33:13.41 UTC9ef22893-9445-4ae4-bf1d-de9ad42d7e502013-02-06 11:17:08.710 UTCb7517a66-bb6a-4969-862d-34921f5f620a2013-02-06 19:57:24.333 UTC13f5ae83-f313-438b-8ca7-5bf638b9579f2013-02-06 13:45:44.424 UTC8333ebc4-ec35-4bba-bbb3-2d89f78bb4322013-02-06 13:08:17.940 UTCPurpose:
Currently, this workflow takes a list of genes and a concept set as input, calculates the matching score between these and finds the concept that contributes the most to the match.
Author comments:
The workflow is in Beta stage. It runs, but needs more testing with different parameter settings. This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/368 for functional gene annotation and knowledge discovery.
2013-02-06 19:57:24.182 UTCf41926bc-1173-4cd6-94ce-34f8bb10e1152013-02-06 14:17:28.659 UTC05e6f84d-b606-4ee1-8dbd-b3fc813a05872013-02-06 18:55:44.517 UTCa950ef98-59af-499c-9fcc-bfe9101ff90d2013-02-06 18:58:12.960 UTCb1337230-2045-44a4-a98e-2710e8286c312013-02-06 11:36:47.649 UTCAuthors:
Kristina Hettne
Contributors:
Reinout van Schouwen, Marco Roos
2013-02-06 19:54:27.608 UTC0f2d6ede-2dba-45ac-ae26-d5164adc885b2013-02-06 11:13:59.426 UTC73bd51a5-526f-4079-a740-b34a1abfe2dd2013-02-06 13:12:36.724 UTC725ac5d6-1a69-4240-9461-f2b5e9bbdf6a2013-02-06 14:02:17.849 UTC37cdecaa-ca6d-4e38-b096-da19215ff26c2013-02-06 11:46:37.385 UTC8e439818-7a37-42e0-90db-7c800600f7362013-02-06 12:49:41.433 UTCc9e941cd-6f71-440b-afd2-04ec26929acc2013-02-06 13:21:01.258 UTC9eedfbed-82d1-4ba5-9c5b-8c92c2c740b92013-02-06 14:00:13.266 UTC8dab1252-b6f6-4c00-8e71-6fb74d9f52532013-02-06 19:44:22.964 UTCfe01d839-8fb8-4243-8b0c-0c03856eab612013-02-06 14:29:55.480 UTCee47e8f0-8809-4408-85df-6369a84484942013-02-06 19:52:38.18 UTCAnnotate a gene list with disease concepts2013-02-06 19:54:56.223 UTCaedced2a-49f2-449b-8a73-e85e495ec0c22013-02-06 11:49:19.279 UTCd2b86eb3-5a8a-4225-9b49-11827828fe402013-02-06 12:41:31.510 UTCdaa2955a-ae29-48d4-845a-4ae77500e7482013-02-06 19:39:14.176 UTCDatabaseID_to_ConceptIDDatabaseID00Identifier for databases, e.g. EG for Entrez Gene
Possible values:
EG, Entrez Gene
2012-06-25 20:38:10.999 UTCEG2012-04-24 23:16:44.86 UTCIDvalue0030642012-04-24 23:17:45.507 UTCIdentifier value, e.g. 3064 for HTT when DatabaseID=EG
2012-06-25 20:37:53.622 UTCConcept_IDshttp://rdf.biosemantics.org/owl/concept#330972122013-02-05 21:21:56.659 UTCConcept Identifiers for the given input, e.g. 3097212 for EG.30642012-04-24 23:19:16.717 UTCmapDatabaseIDToConceptIDsparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://ws.biosemantics.org/ConceptRecognizerService?wsdlmapDatabaseIDToConceptIDsnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050003net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemapDatabaseIDToConceptIDs_inputID0database0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivitydatabase0'text/plain'falseID0'text/plain'falseoutput0'text/xml'0<s:extensions 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typename="conceptSetWrapper" name="return" qname="mapDatabaseIDToConceptIDsResponse>return"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptIDsAsString" qname="conceptSetWrapper>conceptIDsAsString" /></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemapDatabaseIDToConceptIDsparametersmapDatabaseIDToConceptIDs_inputIDmapDatabaseIDToConceptIDs_inputdatabasemapDatabaseIDToConceptIDs_outputinputmapDatabaseIDToConceptIDs_returninputConcept_IDs7c52983e-1954-409c-bbc6-2f026465c5232013-02-06 12:47:08.143 UTCc2cbb1b4-e2b2-4c45-9dfd-5323f702be832012-04-24 23:22:49.83 UTC0b447fad-9299-453c-9195-e00c9fb687a72012-04-24 23:20:02.840 UTC80ee33e8-dddc-4d0f-aef9-ce9790e699042012-04-24 23:12:44.984 UTC7ecf19fa-7ed5-489c-82e5-9b2468795c302012-09-04 11:14:44.543 UTC60ef0156-46c6-4368-a578-e6a26823caba2013-01-28 15:03:01.417 UTCc690ec55-e66d-4cde-a257-f219ab1416792013-02-05 11:51:05.313 UTCd2f0a621-0e45-43b7-bd56-11c61a1c8df92012-07-18 13:13:11.179 UTCPurpose:
This workflow maps input Identifiers, common database identifiers, to the Concept Identifiers from the EMC ontology.
Result:
Concept Identifiers from the EMC ontology.
Resources:
Table of database identifiers and concept identifiers.
Database identifiers from ...
EMC ontology compiled from ...
Comments:
This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery.2012-07-18 13:12:53.96 UTC37daa1ca-9ddd-49a3-a622-41481f0a3c352013-02-05 21:21:58.367 UTCcdf66f51-8d56-4a5f-87c7-5b8dbd434ee82012-07-11 14:23:57.252 UTCAuthors:
Marco Roos on behalf of the BioSemantics group
Contributors:
Web Service by Reinout van Schouwen
Additional annotations by Kristina Hettne2012-07-18 13:12:00.232 UTCDatabaseID_to_ConceptID2012-04-24 23:22:45.412 UTC14fee9a1-cd21-44f2-9f28-4f2362b8d6672012-06-25 20:39:09.656 UTCd5450be7-b43d-4037-9a2c-8fe0d80195132013-02-06 12:37:40.862 UTCExplain_concept_scoresC_ConceptID00The concept id of the C concept.2012-09-11 09:01:25.824 UTChttp://rdf.biosemantics.org/owl/concept#22631262013-02-05 20:09:11.301 UTCcutoff0012012-09-10 15:18:30.889 UTCMaximum number of explanatory concepts to return.2012-09-11 08:30:14.173 UTCA_ConceptID00http://rdf.biosemantics.org/owl/concept#30964312013-02-05 20:09:19.271 UTCThe concept id of the A concept.2012-09-11 09:01:33.736 UTCB_ConceptNameThe concept name of the explanatory B concept.2012-09-11 09:01:44.136 UTCFADS22012-09-10 15:17:05.627 UTCB_ConceptIDThe concept ID of the explanatory B concept.2012-09-11 09:01:40.385 UTChttp://rdf.biosemantics.org/owl/concept#30964312013-02-05 20:09:37.980 UTCB_ConceptContributionThe contribution score, that is, the percentage of the contributions of the individual concepts to the coherence score (the average of the inner product scores of all possible concept pairs within the group).2012-09-11 08:58:01.819 UTC43.362328410148622012-09-10 15:16:19.600 UTCexplainScoresStringInputparameters0parameters00This Web service takes two concept ids as input and returns the top ranking "B" concepts according to Swanson's ABC model of discovery, where the relationships AB and BC are known and reported in the literature, and the implicit relationship AC is a putative new discovery. It might also be the case that AC is already known. In that case AC does not represent a new discovery but will still be returned by the Web service.
The concept contribution is also reported by the Web service. The concept contribution is the percentage of the contributions of the individual concepts to the coherence score (the average of the inner product scores of all possible concept pairs within the group).2012-09-11 08:57:10.939 UTCnet.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://ws.biosemantics.org/ConceptRecognizerService?wsdlexplainScoresStringInputnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeexplainScoresStringInput_inputcutoffValue0conceptCUIsAsString0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivitycutoffValue0'text/plain'falseconceptCUIsAsString0'text/plain'falseoutput0'text/xml'0<s:extensions 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qname="{http://services.conceptrecognizer.lumc.nl/}explainScoresStringInputResponse"><s:elements><s:complextype optional="true" unbounded="false" typename="conceptContributionsWrapper" name="return" qname="explainScoresStringInputResponse>return"><s:elements><s:arraytype optional="true" unbounded="false" wrapped="true" typename=">conceptContributionsWrapper>ConceptContributionTable" name="ConceptContributionTable" qname="conceptContributionsWrapper>ConceptContributionTable"><s:elementtype><s:complextype optional="false" unbounded="false" typename="conceptContribution" name="" qname="{http://services.conceptrecognizer.lumc.nl/}conceptContribution"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptName" qname="conceptContribution>conceptName" /><s:basetype optional="true" unbounded="false" typename="double" name="contribution" qname="conceptContribution>contribution" /><s:basetype optional="true" unbounded="false" typename="int" name="conceptId" 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UTCnet.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivityitem10text/plainjava.lang.Stringtrueitem20text/plainjava.lang.Stringtrueoutput00workflownet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeexplainScoresStringInputparametersexplainScoresStringInput_inputcutoffValueexplainScoresStringInput_inputconceptCUIsAsStringexplainScoresStringInput_outputinputexplainScoresStringInput_returninputreturn_ConceptContributionTable_2input2_ConceptContributionTableinputmakeCommaSeparatedStringitem2makeCommaSeparatedStringitem1B_ConceptNameB_ConceptIDB_ConceptContributionabaeb048-e186-4c8d-92d4-6b32b22603d82012-04-16 13:01:16.427 UTCbb8d1d77-e3d2-4cee-aee9-3cd4e1bd85472012-01-06 12:38:00.681 UTC7a995f89-0c37-48b9-b0f7-8eca5cd364202012-01-06 11:51:06.790 UTC0faa8a91-3a1c-4e03-b74d-f271e7b962902012-04-16 12:55:56.499 UTCa6c096b8-050d-48bf-8b9c-114762aac26d2012-09-07 14:52:03.90 UTC2b762f5e-4473-4d48-b78f-df306600467a2012-09-11 09:11:13.838 UTC13050a9d-bdda-4de5-8bc7-8503457302cd2012-04-16 13:02:36.340 UTC6bab82da-54d0-4bc7-96fd-e5c5d3c6d77f2012-09-07 14:37:53.808 UTC541a7a2d-e3e3-490d-885b-52d653a21d112012-02-03 11:42:15.89 UTC9e4c2fcc-6dcc-46d5-9edd-d7841389ef5c2012-04-17 08:22:27.551 UTC4f826cfe-3950-4151-bbe6-bff67413be512012-09-07 15:22:15.103 UTCPurpose of workflow: This workflow takes two concept ids as input and returns the top ranking "B" concepts according to Swanson's ABC model of discovery, where the relationships AB and BC are known and reported in the literature, and the implicit relationship AC is a putative new discovery. It might also be the case that AC is already known. In that case AC does not represent a new discovery but will still be returned (see workflow example values). The B concepts are returned sorted on the percentage of the contributions of the individual concepts to the coherence score (the average of the inner product scores of all possible concept pairs within the group).
This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery.
2012-09-11 09:11:13.758 UTC7d6ba6db-2552-4c15-b800-1789f5385d442012-09-07 15:18:14.352 UTC1ea652c5-572b-4b0a-b66d-5ae41a7b7fe12013-02-05 09:41:27.678 UTC8f284446-2578-4c4d-b81d-e842a463641b2012-09-07 15:34:00.455 UTC90f0af1e-a653-4a85-889c-4120accdd9d92012-09-07 14:44:36.440 UTC8efd062c-22d8-4fc6-bfe4-ea8f96ba7e2a2012-04-16 12:58:21.8 UTC09802e77-93ac-45ba-9ad5-e7bea33cda8b2013-02-05 20:09:38.174 UTC8d4a9091-0ba9-468e-9883-7b08e5212cd22012-04-16 13:07:32.864 UTC713fa342-cdf4-48b7-850d-abecb37b9b1f2012-09-11 08:58:13.328 UTCc416805f-aa9d-4d44-b434-f253935ed0ef2012-09-11 08:57:11.33 UTCExplain concept scores2012-04-16 13:00:42.27 UTCa260c127-7bbc-4dde-86a9-80647fcbb8622012-09-10 15:18:42.957 UTC88e1d0d3-3377-4a21-a98f-19020444e6862012-09-07 14:58:20.922 UTC89f2da6a-161b-47b1-a048-a65fd35f912c2012-01-06 11:47:16.46 UTC4b937a61-6180-48ce-a679-cf3ed1c8f2082012-09-11 08:58:54.136 UTCfc7ae322-fcac-41c5-b136-0767d52680b02012-03-21 13:53:26.66 UTC142a2c6d-8e96-4c9f-ad64-da97fd4c25972012-09-04 11:16:44.759 UTC3c6eca00-e3a8-46b8-86bd-7c4b48a3ac772012-07-18 13:20:01.872 UTC9a6508bd-87c3-4d9c-99f2-9003b5b57df42012-09-11 09:01:50.31 UTC4bed166d-9815-4a35-a613-869b300b79732012-04-16 13:04:34.678 UTC2b5167d3-3864-46c1-b761-b66ab721da542012-02-03 13:52:44.748 UTCCreator: Reinout van Schouwen on behalf of the BIoSemantics Group
Adaptations by Marco Roos and Kristina Hettne2012-09-11 09:02:52.112 UTCMatch_concept_profilCutoff00The number of resulting matched concepts that will be shown. 2012-04-16 12:36:29.53 UTC12013-02-05 19:53:47.84 UTCMatch_concept_set00The ConceptSet that is to be matched. A list of IDs for the predifined concept sets can be retrieved by running the List Concept Sets workflow (http://www.myexperiment.org/workflows/2999). The example ID corresponds to the concept set GO Biological Processes.2013-02-05 20:18:48.820 UTC52013-01-07 13:18:28.976 UTCQuery_concept_ID00http://rdf.biosemantics.org/owl/concept#42753602013-02-05 20:12:35.528 UTCThe ConceptSet (a list of concept identifiers) to be queried. For example: 42753602012-04-16 12:39:57.499 UTCMatch_concept_ID<http://rdf.biosemantics.org/owl/concept#1156814/>2013-01-29 14:24:54.220 UTCConcept ID of the matched concept.2013-01-29 14:25:01.866 UTCSimilarity_score0.00161509089237915842013-01-29 14:25:31.229 UTCList of similarity scores for the matched concept profiles.2012-09-11 12:29:44.886 UTCQuery_concept_IDgetSimilarConceptProfilesPredefinedparameters0parameters00The Web service takes a (list of) concept identifiers and the ID for the predefined concept set as input and calculates the matching score between the concept profiles of the concepts according to the scaled inner product. A list of IDs for the predifined concept sets can be retrieved by running the List Concept Sets workflow (http://www.myexperiment.org/workflows/2999). The example ID corresponds to the concept set GO Biological Processes.2013-02-05 20:18:25.345 UTCnet.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://ws.biosemantics.org/ConceptRecognizerService?wsdlgetSimilarConceptProfilesPredefinednet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetSimilarConceptProfilesPredefined_inputcutoffValue0conceptSetId0queryConceptProfileList0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivitycutoffValue0'text/plain'falseconceptSetId0'text/plain'falsequeryConceptProfileList0'text/plain'falseoutput0'text/xml'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getSimilarConceptProfilesPredefined" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}getSimilarConceptProfilesPredefined"><s:elements><s:basetype optional="false" unbounded="false" typename="int" name="cutoffValue" qname="getSimilarConceptProfilesPredefined>cutoffValue" /><s:basetype optional="false" unbounded="false" typename="int" name="conceptSetId" qname="getSimilarConceptProfilesPredefined>conceptSetId" /><s:basetype optional="true" unbounded="false" typename="string" name="queryConceptProfileList" qname="getSimilarConceptProfilesPredefined>queryConceptProfileList" 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typename="getSimilarConceptProfilesPredefinedResponse" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}getSimilarConceptProfilesPredefinedResponse"><s:elements><s:complextype optional="true" unbounded="false" typename="matchingResult" name="return" qname="getSimilarConceptProfilesPredefinedResponse>return"><s:elements><s:arraytype optional="true" unbounded="false" wrapped="true" typename=">matchingResult>MatchConceptProfileList" name="MatchConceptProfileList" qname="matchingResult>MatchConceptProfileList"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="similarityScoreLists" name="SimilarityScoreLists" qname="matchingResult>SimilarityScoreLists"><s:elementtype><s:complextype optional="false" unbounded="false" typename="scoreListImpl" name="" qname="{http://services.conceptrecognizer.lumc.nl/}scoreListImpl"><s:elements><s:arraytype optional="true" unbounded="true" wrapped="false" typename="stringDoubleTuple" name="QueryScoreTupleList" qname="scoreListImpl>QueryScoreTupleList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="stringDoubleTuple" name="" qname="{http://services.conceptrecognizer.lumc.nl/}stringDoubleTuple"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="queryConceptID" qname="stringDoubleTuple>queryConceptID" /><s:basetype optional="true" unbounded="false" typename="double" name="score" qname="stringDoubleTuple>score" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:basetype optional="true" unbounded="false" typename="string" name="conceptId" qname="scoreListImpl>conceptId" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" 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typename="stringDoubleTuple" name="QueryScoreTupleList" qname="scoreListImpl>QueryScoreTupleList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="stringDoubleTuple" name="" qname="{http://services.conceptrecognizer.lumc.nl/}stringDoubleTuple"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="queryConceptID" qname="stringDoubleTuple>queryConceptID" /><s:basetype optional="true" unbounded="false" typename="double" name="score" qname="stringDoubleTuple>score" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:basetype optional="true" unbounded="false" typename="string" name="conceptId" qname="scoreListImpl>conceptId" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename=">matchingResult>SummedSimilarityScoreList" name="SummedSimilarityScoreList" qname="matchingResult>SummedSimilarityScoreList"><s:elementtype><s:basetype optional="false" 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optional="false" unbounded="false" typename="scoreListImpl" name="" qname="{http://services.conceptrecognizer.lumc.nl/}scoreListImpl"><s:elements><s:arraytype optional="true" unbounded="true" wrapped="false" typename="stringDoubleTuple" name="QueryScoreTupleList" qname="scoreListImpl>QueryScoreTupleList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="stringDoubleTuple" name="" qname="{http://services.conceptrecognizer.lumc.nl/}stringDoubleTuple"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="queryConceptID" qname="stringDoubleTuple>queryConceptID" /><s:basetype optional="true" unbounded="false" typename="double" name="score" qname="stringDoubleTuple>score" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:basetype optional="true" unbounded="false" typename="string" name="conceptId" qname="scoreListImpl>conceptId" 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13:52:40.391 UTCcc6b35c6-0d92-4ef7-ae5b-08eab3af670c2013-01-07 13:21:45.613 UTCdafd97bb-bd4c-4540-b335-d9cfe2d841082012-04-16 15:04:13.913 UTC6abd5004-cd71-47bb-8619-fe764fbe1a8c2013-02-06 13:57:55.835 UTC8bdb17e0-10d5-42c5-9649-595b5b3ca2262012-09-04 11:16:15.351 UTC46181b16-64e9-40aa-8dde-b32a9478fe1d2011-09-27 15:29:17.819 UTCfafb8d94-026f-4044-b3ce-866fc199229b2011-09-28 12:06:54.60 UTC680aa556-740a-433c-b63e-82a270a9d9e32013-01-29 15:48:25.704 UTC0c468adb-8c4b-4f37-839e-6d2fe21d821b2013-02-06 13:58:23.234 UTCae37940d-e39c-43c2-80bf-512e607102012012-04-16 12:45:48.511 UTC98159653-b95c-4a97-b6b3-b400a68f0dc42013-01-29 14:17:24.662 UTCAuthors:
Kristina Hettne, Marco Roos
Contributors:
Reinout van Schouwen2012-06-24 20:56:28.572 UTC1d5bb33c-d18f-4d9c-9ead-487ab5271b7a2011-09-27 15:37:33.997 UTC19844d48-41a3-49e5-8cd3-5c3ccc40ec002013-01-07 13:19:35.160 UTC5b1481fe-3fb7-4dfd-b527-d97b565035062013-02-06 12:47:43.7 UTC33f8a974-4c7a-4f27-93f7-a4eb2ed293d42013-02-06 13:56:08.836 UTC487ca7a4-63fa-45f9-baab-8f9a053ca9d02012-04-16 12:50:38.225 UTC60d3ffca-7a97-485f-a391-6f8273236e1c2013-02-01 11:26:19.951 UTC233c6660-ebf6-47c8-af02-b1884424153d2012-09-11 12:12:26.526 UTCa78cb530-6e91-48ac-8d8b-e6bc9ce7b0fa2013-01-29 14:25:31.386 UTCe3d98432-1b19-474a-8c12-ed90f6aa23e82013-02-05 20:13:04.448 UTC91ab33da-4da0-4e22-9542-7994c993b96a2013-01-29 16:08:36.560 UTC4eb7b1fd-ec11-4fff-8a9b-ed9602b6bf8d2013-02-05 20:16:31.628 UTC0dcad6f0-b77c-4d5d-ae1b-893a7b2436a62011-09-28 12:12:42.334 UTCda482794-4042-408d-adc4-c035dcb831ab2012-04-16 12:41:12.260 UTC6036660d-2ac0-4369-a7f7-d208a0a262652012-09-11 12:31:12.75 UTC0d2ee2ad-e803-4529-afc2-e15bcd124a0c2013-01-29 14:14:04.577 UTC3869f1dd-8db7-4881-b73a-4d55c99c60892013-02-01 15:53:09.746 UTC09430282-326d-4c5b-85a8-28ddfc97753e2011-09-27 15:31:47.87 UTCabf2582f-e23f-40ff-b26a-c51da6f9e8f52013-02-05 11:11:56.753 UTC25ac05cb-87b1-4cee-926a-4fb5c6662b8f2013-02-05 20:18:50.908 UTC788f406a-4ccf-40ce-82e0-cf5aad9169782013-02-06 12:40:31.874 UTC681cb800-d7cb-4786-8c64-585df6b607c72013-02-05 19:53:51.192 UTCe7d32565-d838-4bd0-987d-f03c4093d3452013-01-29 14:21:26.174 UTC526ee9ee-6592-4472-90d4-f392659ea5842013-01-29 12:44:50.692 UTCffd57175-7b65-4edb-9086-42bad4170b462011-09-27 13:41:33.82 UTC4d330136-ca78-4fa0-ad95-0d34b85f8a762011-09-20 15:56:44.26 UTC477ba81b-f13d-41f2-ba19-e19f6104e36e2012-09-11 12:14:41.164 UTCe48487a3-446f-42a1-9fcc-d820a9498ff02012-07-18 13:14:50.306 UTCMatch concept profiles with predefined set2013-01-07 13:20:03.887 UTCabeb3495-f850-47e4-bc90-018b365840922011-09-28 12:24:29.380 UTC9e39fe6a-c3da-4e04-a3ee-8c8dee6aa9162013-01-28 15:31:38.841 UTCde3149d9-6f9a-49cd-a542-91c18f65109d2012-09-11 12:27:01.860 UTC494bf485-3d60-4900-88f6-060f54ef39692013-01-29 13:27:18.126 UTC9a1764af-8145-4c13-a849-38a031e6f2dd2011-09-28 12:26:45.132 UTCPurpose of workflow: The workflow can be used to match a set of concept profiles with another set of concept profiles. The result is a list of concepts ordered by their match to the query concept profiles.
The workflow matches two sets of concept profiles. At the time of writing the concepts are derived from human, rat, and mouse terminologies, ontologies, and database identifiers. The profiles are lists of concepts ranked by their association with the identifying concept, as determined by co-location statistics computed from MedLine (up until 2009 at the time of writing).
Author's comments: This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery.
2012-09-11 12:07:27.213 UTCdacab209-3218-4181-a2f4-eaacfb1022b12013-02-04 10:17:42.374 UTC0e2bcc6a-21cb-4a66-a50c-42fd8b2226aa2013-01-07 13:15:58.306 UTC843e31e3-bf17-4604-a2b6-d3ff38107f9f2013-02-06 13:57:05.208 UTC55a9d4ab-19ee-4042-bf3d-5fabb52a3ab22012-06-24 20:56:30.877 UTC7986f41c-7556-45d9-bcb3-f557b69f3acc2012-04-15 20:28:43.911 UTC1b7115f7-7832-4081-88df-c6ce4775238f2011-09-28 11:35:31.328 UTC15145a87-30e2-4e04-97a9-10572ff64aae2011-09-28 11:37:06.330 UTCea38018e-ee90-4ccb-ab8e-78eeec907cad2011-09-28 12:02:39.57 UTCdacab209-3218-4181-a2f4-eaacfb1022b12013-02-05 11:18:43.126 UTCc55d2bf1-a3b9-46b1-a486-97b4b03eca202012-04-16 15:03:34.648 UTCGet_concept_informatConcept_ID00http://rdf.biosemantics.org/owl/concept#30926192013-02-05 20:07:38.791 UTCConcept ID of the concept to retrieve name and definition for.2012-07-04 11:50:31.405 UTCConcept_nameGLS22012-07-04 11:55:50.464 UTCThe name of the concept.2012-07-04 11:51:39.675 UTCgetConceptProfileparameters0parameters00This Web service returns the concept profile for a given concept ID.2012-09-11 12:51:04.847 UTCnet.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://ws.biosemantics.org/ConceptRecognizerService?wsdlgetConceptProfilenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetConceptProfile_inputconceptId0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivityconceptId0'text/plain'falseoutput0'text/xml'0<s:extensions 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qname="{http://services.conceptrecognizer.lumc.nl/}getConceptProfileResponse"><s:elements><s:complextype optional="true" unbounded="false" typename="conceptProfileWrapper" name="return" qname="getConceptProfileResponse>return"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptId" qname="conceptProfileWrapper>conceptId" /><s:basetype optional="true" unbounded="false" typename="string" name="name" qname="conceptProfileWrapper>name" /><s:basetype optional="true" unbounded="false" typename="string" name="definition" qname="conceptProfileWrapper>definition" /><s:arraytype optional="true" unbounded="false" wrapped="true" typename=">conceptProfileWrapper>ConceptVector" name="ConceptVector" qname="conceptProfileWrapper>ConceptVector"><s:elementtype><s:complextype optional="false" unbounded="false" typename="stringDoubleTuple" name="" qname="{http://services.conceptrecognizer.lumc.nl/}stringDoubleTuple"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="queryConceptID" qname="stringDoubleTuple>queryConceptID" /><s:basetype optional="true" unbounded="false" typename="double" name="score" qname="stringDoubleTuple>score" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetConceptProfile_returninput0name00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivityinput0'text/xml'java.lang.StringfalseconceptId0'text/plain'0name0'text/plain'0definition0'text/plain'0ConceptVector0'text/xml'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="true" unbounded="false" typename="conceptProfileWrapper" name="return" qname="getConceptProfileResponse>return"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptId" qname="conceptProfileWrapper>conceptId" /><s:basetype optional="true" unbounded="false" typename="string" name="name" qname="conceptProfileWrapper>name" /><s:basetype optional="true" unbounded="false" typename="string" name="definition" qname="conceptProfileWrapper>definition" /><s:arraytype optional="true" unbounded="false" wrapped="true" typename=">conceptProfileWrapper>ConceptVector" name="ConceptVector" qname="conceptProfileWrapper>ConceptVector"><s:elementtype><s:complextype optional="false" unbounded="false" typename="stringDoubleTuple" name="" qname="{http://services.conceptrecognizer.lumc.nl/}stringDoubleTuple"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="queryConceptID" qname="stringDoubleTuple>queryConceptID" /><s:basetype optional="true" unbounded="false" typename="double" name="score" qname="stringDoubleTuple>score" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetConceptProfileparametersgetConceptProfile_inputconceptIdgetConceptProfile_outputinputgetConceptProfile_returninputConcept_name6a41503c-d915-4eac-998e-0d10ee8f32f12013-02-05 20:07:44.871 UTCdea60608-70c7-4cf0-a8da-8513eb1a440a2012-09-04 11:17:36.783 UTCa2ecda87-b5b6-473a-af29-b9fcf32ea7072012-09-11 12:40:55.902 UTCGet concept information2012-07-04 11:53:15.951 UTCCreator:
Kristina Hettne on behalf of the BioSemantics group
Contributions:
Web services by Reinout van Schouwen2012-07-18 13:22:40.527 UTC04d2b539-0ecf-47a2-b036-73e97581556f2012-07-04 11:56:13.312 UTC2824bc65-af91-41c0-8912-e24151314a572012-09-11 12:51:06.419 UTCe68e4b96-f69b-4847-a2fc-eb939e3d146e2013-02-06 14:15:07.963 UTCThe workflow takes a concept ID as input and returns the ID, definition and name of the concept.
This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery.2012-07-18 13:22:23.330 UTCbe71b208-25eb-473e-938d-4ad108bb3a292013-02-06 14:16:04.795 UTC80bc71ed-b511-4824-98e2-3e5add19aaae2012-09-07 14:29:24.729 UTC3afe257a-1246-4267-be82-ccb4203af53f2013-02-04 14:49:02.214 UTCc6eaa639-5ee7-474e-9dbb-401927d650302012-09-11 12:49:35.323 UTC0f9f0834-7609-4af4-b3dd-6a9452cda1232012-09-11 12:44:40.991 UTCb31a4602-eda2-485b-ad82-07db5fe820682012-07-04 11:54:39.48 UTCcf644a3e-3942-4c42-b8c7-2f834fd110d42012-07-18 13:22:54.983 UTC4b5150df-f12d-4f9a-a51e-a655e4c3cba12013-02-04 14:41:45.41 UTC