SNPs_to_Concept_Set_SNP_ID00 ID for the SNP (dbSNP format (http://www.ncbi.nlm.nih.gov/snp)). 2012-06-20 15:17:25.383 UTC rs2657879 2012-06-20 13:37:18.848 UTC EntrezGene_database_type_ID00 EG 2012-06-20 14:32:52.489 UTC The ID for the EntrezGene database (Erasmus MC ontology format). 2012-06-25 12:35:49.147 UTC Set_width00 The allows the user to set the flanking width for the gene for determining SNPs. 2012-09-11 11:12:10.52 UTC 100000 2012-09-11 11:12:17.975 UTC Match_concept_set00 ID of the predefined concept set to match with. These IDs can be retrieved by running the List Concept Sets workflow (http://www.myexperiment.org/workflows/2999). The example ID corresponds to the concept set GO Biological Processes. 2013-02-05 12:13:53.474 UTC 5 2013-02-05 12:13:59.34 UTC Matched_concepts_cutoff00 Max number of concepts to return from the concept profile matching procedure. 2013-02-05 12:13:08.874 UTC 1 2013-02-05 12:13:11.666 UTC Co_occurring_documents_cutoff00 1 2013-02-05 12:14:25.107 UTC Max number of co-occurring documents to return for a concept pair. 2013-02-05 12:15:11.105 UTC Explained_concepts_cutoff00 1 2013-02-05 12:11:51.443 UTC Max number of explanatory concepts to return for a concept profile match. 2013-02-05 12:11:48.4 UTC Similarity_score Concept match similarity score from the matching procedure. 2013-02-05 12:19:18.72 UTC 2.689709811254242E-4 1.4602940663887876E-4 2.5138175063858174E-4 3.035844663481836E-4 2013-02-05 19:14:42.22 UTC Match_concept_ID IDs for the concepts from the concept profile match. 2013-02-05 12:20:06.783 UTC <http://rdf.biosemantics.org/owl/concept#1523019/> <http://rdf.biosemantics.org/owl/concept#1159571/> <http://rdf.biosemantics.org/owl/concept#1156814/> <http://rdf.biosemantics.org/owl/concept#1155260/> 2013-02-05 19:13:59.580 UTC Co_occurring_document_title The document IDs for which the query and the match concept co-occur. The example IDs refers to PubMed IDs. 2013-02-05 12:20:50.566 UTC 18029913 18787121 17237322 2013-02-05 12:21:57.447 UTC Co_occurring_document_ID Entrainment of the Drosophila circadian clock: more heat than light. Dynamic control of slow water transport by aquaporin 0: implications for hydration and junction stability in the eye lens. Energy metabolism in developing chicken lymphocytes is altered during the embryonic to posthatch transition. 2013-02-05 12:21:40.55 UTC The document titles for which the query and the match concept co-occur. 2013-02-05 12:21:05.975 UTC Match_concept_name Names for the concepts from the concept profile match. 2013-02-05 12:20:11.759 UTC circadian behavior water transport glutamine metabolic process regulation of complement activation 2013-02-05 12:22:45.270 UTC Query_concept_name Names of the genes the SNPs were mapped to (only concepts with concept profiles are shown). 2013-02-05 12:16:07.435 UTC TIMELESS MIP26 GLS2 RBMS2 2013-02-05 19:12:13.968 UTC Explanatory_concept_name The concept names of the explanatory concepts. 2013-02-05 12:17:14.521 UTC tim aquaporin activity D-glutamine CD55 2013-02-05 12:23:26.990 UTC Explanatory_concept_contribution The contribution scores for the explanatory concepts, 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). 2013-02-05 12:16:46.640 UTC 30.8639258146286 44.40696835517883 42.68406629562378 48.19859266281128 2013-02-05 12:23:41.822 UTC Explanatory_concept_ID http://rdf.biosemantics.org/owl/concept#3055620 http://rdf.biosemantics.org/owl/concept#1753274 http://rdf.biosemantics.org/owl/concept#4275360 http://rdf.biosemantics.org/owl/concept#3095008 2013-02-05 19:33:08.193 UTC The concept IDs of the explanatory concepts. 2013-02-05 19:32:47.1 UTC Query_concept_ID Concept IDs of the genes the SNPs were mapped to (only concepts with concept profiles are shown). 2013-02-05 12:15:44.881 UTC http://rdf.biosemantics.org/owl/concept#3108483 http://rdf.biosemantics.org/owl/concept#3088120 http://rdf.biosemantics.org/owl/concept#3092619 http://rdf.biosemantics.org/owl/concept#3088115 2013-02-05 19:10:23.169 UTC SNP_ID2EntrezGene_IDSNP_ID0set_width0EntrezGene_ID22 Purpose of component in workflow: This component maps a SNP ID to EntrezGene IDs. 2012-06-25 20:24:42.884 UTC net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeEntrezGeneID_to_ConceptIDDatabaseID0IDvalue0Concept_IDs00 Purpose of component in workflow: The purpose of this component (nested workflow) here is to map Gene Ontology and 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. 2012-07-11 15:11:56.573 UTC net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFilter_genes_with_profilesConcept_ID0Concepts_with_profiles11 Purpose of component in workflow: The purpose of this component (nested workflow) here is to remove concepts that have no concept profile in the concept profile database, since only concepts with a concept profile can be used for concept profile matching. 2013-02-05 16:34:14.236 UTC net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeMatch_concept_profilesMatch_concept_set0Cutoff0Query_concept_ID0Similarity_score11Match_concept_ID11 Purpose of component in workflow: The purpose of this component (nested workflow) in this workflow is to match the concept profiles of genes identified by proximity to SNPs, to the profiles of Gene Ontology (GO) concepts (from the GO process branch). The assumption is that the genetic variation close to these genes indicate genetic variation that is potentially causative for the phenotype under study. Results: The results of this component are biological processes (GO concepts) associated with genes close to input SNPs, ranked in the order of the match score between the input concepts. The results suggest which biological processes are associated with the putative genetic causes as indicated by the identified genes associated with the identified SNPs. 2013-02-05 18:54:49.443 UTC net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFind_co_occurring_documentsCutoff_value0ConceptID_11ConceptID_21Document_title33Document_ID33 Purpose of component in workflow: This component retieves the co-occuring documents for the query concept and the matched concept. 2013-02-05 18:55:42.416 UTC net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGet_match_concept_nameConcept_ID0Concept_name00 Purpose of component in workflow: To retrieve the name of the concept from the ontology. 2013-02-05 18:56:56.393 UTC net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGet_concept_ID_and_nameConcept_ID0Concept_name00Concept_ID00 Purpose of component in workflow: To retrieve the name of the concept from the ontology. 2013-02-05 18:56:44.407 UTC net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExplain_concept_scorescutoff0A_ConceptID0C_ConceptID0B_ConceptContribution11B_ConceptName11B_ConceptID11 Purpose of component in workflow: This component retieves the concepts contributing most to the match perfomed in the Match_concept_profiles component. 2013-02-05 18:55:19.528 UTC net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_concept_ID_listinputlist2outputlist11 This service flattens the inputlist by one level. It returns the result of the flattening. 2013-02-05 19:36:13.112 UTC net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity inputlist 2 l(l('')) [B true outputlist 1 l('') 1 workflow org.embl.ebi.escience.scuflworkers.java.FlattenList net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_Concept_name_listinputlist2outputlist11 This service flattens the inputlist by one level. It returns the result of the flattening. 2013-02-05 19:36:18.256 UTC net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity inputlist 2 l(l('')) [B true outputlist 1 l('') 1 workflow org.embl.ebi.escience.scuflworkers.java.FlattenList net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_match_concept_ID_listinputlist2outputlist11 This service flattens the inputlist by one level. It returns the result of the flattening. 2013-02-05 19:36:07.688 UTC net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity inputlist 2 l(l('')) [B true outputlist 1 l('') 1 workflow org.embl.ebi.escience.scuflworkers.java.FlattenList net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSNP_ID2EntrezGene_IDSNP_IDSNP_IDSNP_ID2EntrezGene_IDset_widthSet_widthEntrezGeneID_to_ConceptIDDatabaseIDEntrezGene_database_type_IDEntrezGeneID_to_ConceptIDIDvalueSNP_ID2EntrezGene_IDEntrezGene_IDFilter_genes_with_profilesConcept_IDEntrezGeneID_to_ConceptIDConcept_IDsMatch_concept_profilesMatch_concept_setMatch_concept_setMatch_concept_profilesCutoffMatched_concepts_cutoffMatch_concept_profilesQuery_concept_IDFilter_genes_with_profilesConcepts_with_profilesFind_co_occurring_documentsCutoff_valueCo_occurring_documents_cutoffFind_co_occurring_documentsConceptID_1Match_concept_profilesMatch_concept_IDFind_co_occurring_documentsConceptID_2Filter_genes_with_profilesConcepts_with_profilesGet_match_concept_nameConcept_IDMatch_concept_profilesMatch_concept_IDGet_concept_ID_and_nameConcept_IDFilter_genes_with_profilesConcepts_with_profilesExplain_concept_scorescutoffExplained_concepts_cutoffExplain_concept_scoresA_ConceptIDFilter_genes_with_profilesConcepts_with_profilesExplain_concept_scoresC_ConceptIDFlatten_match_concept_ID_listoutputlistFlatten_concept_ID_listinputlistGet_concept_ID_and_nameConcept_IDFlatten_Concept_name_listinputlistGet_concept_ID_and_nameConcept_nameFlatten_match_concept_ID_listinputlistMatch_concept_profilesMatch_concept_IDSimilarity_scoreMatch_concept_profilesSimilarity_scoreMatch_concept_IDMatch_concept_profilesMatch_concept_IDCo_occurring_document_titleFind_co_occurring_documentsDocument_titleCo_occurring_document_IDFind_co_occurring_documentsDocument_IDMatch_concept_nameGet_match_concept_nameConcept_nameQuery_concept_nameFlatten_Concept_name_listoutputlistExplanatory_concept_nameExplain_concept_scoresB_ConceptNameExplanatory_concept_contributionExplain_concept_scoresB_ConceptContributionExplanatory_concept_IDExplain_concept_scoresB_ConceptIDQuery_concept_IDFlatten_concept_ID_listoutputlist 574cdcb3-529b-414c-8d27-c577a2a3e19c 2013-02-04 14:43:47.363 UTC a6d386e3-9404-4299-814d-07e20ced15d0 2012-09-11 12:54:25.760 UTC 5c98679f-949c-472a-8ab7-22c0013a1045 2012-06-20 12:55:14.538 UTC d063979e-1984-4572-aa4b-ee0fa5239443 2012-07-18 13:25:29.879 UTC 1b7ef364-6500-4ee4-b82d-aa5d6081c42d 2013-02-04 14:15:34.22 UTC 92abab27-280e-457d-a60b-986ec4b53de3 2013-02-05 19:34:10.47 UTC baba66e2-155d-458c-86ce-c3d20f3bcdac 2013-01-28 16:26:25.713 UTC caf05cc4-68f8-46f6-bdc6-3b140b207346 2013-02-05 19:27:38.962 UTC 5c9f56ec-5fa4-46eb-9b49-05f99d24e3ee 2012-09-11 15:21:33.102 UTC e9a45dfa-bfae-4220-97bf-1c6d163a3e49 2012-06-25 21:25:02.684 UTC 50cd099f-d399-4e02-a4c8-870716274d92 2012-07-03 15:07:35.937 UTC 8a1c891f-626c-4eec-ad0a-2037af351869 2012-06-25 12:40:54.246 UTC fc5f9431-f6d8-4372-b2fc-df52b5b7517d 2013-02-04 14:57:30.952 UTC a1998c75-395a-43a8-bac1-41d27db56864 2013-02-05 16:34:19.12 UTC 31345088-55d0-4330-8a97-cff2d81405f5 2012-09-11 11:12:18.177 UTC 78a68b62-d77c-4998-b032-041fda263d03 2012-09-12 12:59:34.796 UTC 381a5e2b-e86e-4d6f-8458-eacc9250c96d 2013-02-04 14:13:52.886 UTC 4eef1006-16ee-4410-8b29-1f39b0b30a14 2013-02-05 11:30:27.74 UTC 9c29ff3b-6799-4086-b61b-3f5ddea195ad 2013-02-05 12:24:00.388 UTC ffafa1a3-9198-4a07-81e5-f7443b9776c7 2012-07-11 15:15:22.568 UTC 42382374-0201-4786-a335-25db83eadff2 2012-06-20 14:54:43.422 UTC 7c6624ce-6248-4a90-89a7-d55cde995e9f 2013-02-05 09:43:39.757 UTC 35f8e419-c47b-4d49-8ba7-e7c0ef59955e 2013-02-05 09:27:31.548 UTC 38e446d2-7e40-4b6b-a4c7-2597aab3cb1e 2012-06-20 14:53:07.143 UTC SNPs to Concept Set through Concept Profile Matching v2 2013-01-09 08:56:40.72 UTC 31c7fb0f-67df-4ac2-8885-406acbcf6c45 2012-09-04 09:41:50.288 UTC ec1a8ee4-a30e-4050-a880-c4398dacfb3b 2012-07-11 13:41:54.48 UTC cab2e912-2388-43e9-9e31-f2e0743a31cc 2013-02-05 10:56:52.361 UTC e45e1e2f-7573-4714-821f-314aa36f31d0 2012-07-04 12:01:02.382 UTC 41f7efc1-6d56-4034-9955-b23fd9d48ad9 2012-07-16 14:35:23.279 UTC f38cf673-7865-49c5-97b1-d60d7d2bc5cf 2013-02-05 11:12:07.679 UTC 4941fa84-f47f-4029-a615-27647edea50b 2013-01-29 15:44:46.355 UTC b1e9fdfc-e7ec-4375-93dc-ecbc241a6257 2013-01-29 16:22:42.695 UTC ed1e0f31-ddd6-4d2f-8ccd-7bb6700b3b45 2012-09-05 07:18:19.98 UTC fce68cee-1931-4cd4-870b-3a1c0161ea31 2012-06-20 15:17:27.479 UTC 3814ffc0-f31a-4c96-820e-7cfba060cfd5 2012-06-25 12:17:59.1 UTC 69d2b07d-1b28-4c30-ada7-202b4df5c8eb 2012-07-11 14:56:13.37 UTC abbd18c4-a83e-4ae4-93e9-4d577f05e9e5 2013-02-05 11:18:53.955 UTC f08fe7b1-b124-4428-aa7f-aa4148445c24 2013-01-29 14:49:12.507 UTC fd21446e-6061-4805-b414-ac7cc30de529 2013-02-01 11:26:28.673 UTC 2dc8d590-d845-4bde-8cd1-369e4f1503a9 2012-06-20 13:35:14.359 UTC f3137546-0733-49fb-bcad-fdf670a85c63 2013-02-05 19:37:51.70 UTC 1bc8cbea-e850-4e43-917f-ad233066686b 2012-09-11 12:39:42.431 UTC 65c0bb3a-4988-4234-bc43-f6a33084f7b4 2012-09-05 11:23:28.93 UTC 5075e001-4308-4145-b01b-163440ed659c 2013-02-05 19:01:20.540 UTC 2a6fb5b7-a2d0-4e3f-ab37-69e93c57a5d8 2013-02-04 14:50:05.607 UTC 9cfa9e29-4cd6-4ea0-91ae-b50cbb6298db 2012-09-11 13:02:19.614 UTC d207bb24-4f15-452e-82a4-addf9ed71b71 2012-07-03 10:30:04.342 UTC f95aab4d-710a-46ed-8d23-d248d5e4ac89 2012-06-25 11:38:25.616 UTC 8aba1fcc-9e6e-4b3a-94e2-15c3734571a7 2012-10-18 14:07:51.850 UTC 717e09ce-abfa-4f33-aa13-e916319a330a 2012-09-12 07:06:36.668 UTC 10f45a70-24ed-46a0-94f5-27a8f45b195a 2013-02-04 11:02:18.123 UTC f53cdcc9-070e-4d5e-adf5-06b9bd9990f5 2012-07-18 13:29:42.117 UTC 8e7a0dad-8bcb-4808-a8ef-fc206aa67397 2012-07-11 14:25:39.502 UTC 8db56f8b-2734-4bc1-a6a2-cc39b4f04819 2012-06-26 09:36:16.284 UTC 3705a5da-0d54-42e7-8f69-5fcf173679c6 2013-02-05 19:23:31.320 UTC 689aca1a-e790-46da-89b4-8dd78a849d73 2013-02-01 15:53:13.435 UTC cb173e1d-c9f6-44fd-8e4a-feed0205ac27 2013-01-28 15:07:36.514 UTC feff77fe-9dd9-43cd-9f34-150ff8535ecc 2013-01-29 14:44:48.318 UTC f250679d-8be4-4282-bc0c-718b34b3cf90 2012-07-11 15:18:04.57 UTC b6e51879-3d2b-49d1-889b-ba650aa73b38 2012-09-05 08:53:51.612 UTC 730ce424-62f4-4fc4-8392-f20d2be09da4 2012-09-12 10:44:52.756 UTC 31d2984c-7a07-4f6a-a9dc-ebb3772c1751 2012-09-07 15:00:44.730 UTC 38349196-b8df-45ba-be5b-8a1f1d62e1aa 2013-02-04 14:53:22.525 UTC dd3da84c-4247-4a31-a533-cf055577d81b 2013-02-05 11:42:37.21 UTC 63b150c1-06b2-4353-bf3c-a2fcf48d6f48 2012-09-07 15:04:00.35 UTC Authors: Kristina Hettne, Marco Roos Contributors: Reinout van Schouwen, Marco Roos 2012-06-24 20:50:02.542 UTC 3422a432-9059-4f9b-a194-7e31a73e5b1e 2012-09-12 13:39:27.31 UTC 1e1fef40-ce71-4601-9138-53cf866679b2 2012-09-12 07:09:35.368 UTC c44b9143-48dd-4172-b44d-6d39cb57b421 2012-09-12 10:06:17.872 UTC 9abaa51a-ea9b-480f-970a-812916f1c4a7 2013-02-04 14:49:09.919 UTC c7f596eb-b461-4a82-acde-e369c09d8806 2013-02-05 09:54:26.514 UTC 92b312b4-d97a-4767-a54f-6d1e2ff411fb 2013-01-28 15:17:26.598 UTC 48c1a107-fc59-43a2-b40b-3193dbee9621 2013-02-04 10:34:10.48 UTC 84d272a3-ab36-4aa1-ba06-e5d4be6ddaae 2012-06-20 13:42:04.903 UTC 25736105-7e2a-4169-a17c-f6df342feb91 2013-02-05 18:58:33.132 UTC f7d6584f-421e-41c6-b70c-bc019cf35672 2012-06-20 13:27:25.847 UTC bada19cd-999b-4c78-996a-a8cf435bc1e8 2012-06-20 14:43:29.27 UTC Purpose: Currently, this workflow takes one SNP and a concept set as input, calculates the matching score between these, finds co-occuring documents between the query concept and the match concept, finds the concept that contributes the most to the match, and the documents that support this finding. 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/282 for functional gene and SNP annotation and knowledge discovery. 2012-07-18 13:29:38.141 UTC e06f04ed-8f2b-43b6-b73c-0c1db8ecb268 2012-06-25 11:42:30.855 UTC 42cc0e98-a177-4766-ade6-c4f6b634c96c 2013-02-05 11:21:37.942 UTC dd3d3cf8-5693-4031-94a2-688b70d8375f 2012-06-24 20:57:10.828 UTC 4c055cd0-f134-4be3-a41a-11aad85725e1 2013-02-05 20:20:00.52 UTC 3a597170-9a73-40dc-822e-7411a48c84a0 2013-01-09 08:59:58.479 UTC 6157699b-3fab-429a-a253-081473d7f7b9 2013-02-05 20:47:07.598 UTC c9ce92ff-38c8-4b8b-84bb-df60c09e705d 2012-09-11 15:29:14.683 UTC 081ca849-6a33-4ce7-807d-088976f280ff 2012-09-12 12:36:07.673 UTC 02cbb28d-4940-47c4-a45d-8579a2f91d5d 2013-01-29 15:50:22.589 UTC 38d29248-0454-4b55-baa3-d24fab456b1c 2012-09-12 10:54:47.812 UTC bc2328b4-2251-49e7-92a3-63c971b773c7 2012-07-11 12:57:09.537 UTC f470d697-590a-4a5c-a5ac-0421a2a5779f 2012-06-25 21:42:16.998 UTC 21363a00-84f3-40e9-b676-4e5da44ee4b8 2013-01-29 15:46:43.251 UTC 6c275f7a-163e-41ce-913a-1074939d1b4b 2013-02-05 12:21:26.778 UTC 6f2a1eb8-b131-4182-852d-a7c38065b6f5 2013-02-05 16:28:25.603 UTC 0d0232fd-9c2c-4f97-994b-a7b4fade3aeb 2012-06-25 12:46:15.951 UTC d415cfa3-3d04-4dd4-b1cb-b1c8658d5cc4 2012-06-25 10:06:26.773 UTC babf573f-83d7-4304-a59f-f1d53a19c4cc 2012-09-11 10:06:58.293 UTC 349299f5-c1d4-41f9-a3c8-256fb4dedecb 2012-06-20 14:50:32.447 UTC 9a17df2c-d08c-4ad8-b70d-17c26b2b2e67 2012-09-11 14:57:41.380 UTC aaa51b39-b160-4e85-a78c-cf6387ff3073 2012-07-11 12:59:11.88 UTC 5552b01c-5913-4fc5-908f-64bcb8b9f94d 2012-07-11 13:48:59.422 UTC e6475d43-1bdc-4f31-a4b6-0d9642f617fa 2013-02-05 09:07:27.795 UTC 07e1051d-482b-431c-8bae-f8b65ec6a0a0 2012-06-25 12:47:08.190 UTC e90f9090-4f42-42c7-94a5-6296d92f7acb 2012-06-25 12:08:23.148 UTC 7471d9d8-88d1-4d96-9719-b347cd36c2ff 2012-06-20 14:38:14.733 UTC 8b9aed18-36d1-4f57-a885-b2a7c2bac873 2012-07-04 08:59:08.521 UTC b8f53807-cfa6-40d1-acfb-9aa59d38fa74 2012-06-23 14:14:48.33 UTC 724f40c1-2c66-4d0b-ab41-59eb2b0f8383 2012-06-24 20:54:25.360 UTC 81c79d04-e062-47ba-a22b-ddec56289baa 2013-01-29 16:09:05.655 UTC fe747322-34f8-42fe-9aa8-aa202d6c6be9 2013-02-05 15:32:38.623 UTC 616f2861-9708-4254-8ead-11fd31cdefe5 2013-02-05 11:35:58.360 UTC 33f1f0d9-6566-44e8-8ddc-7791fe15aee2 2013-02-05 09:17:15.885 UTC 3edb70a4-e66f-4b96-8e12-3e440266e375 2013-02-05 11:55:18.600 UTC e2ba0280-202b-4d6d-821b-b3539384e237 2013-01-29 14:26:51.986 UTC e6603d60-cfc2-4dc7-a8e4-3fbd83af3879 2012-06-25 12:15:42.217 UTC 460d423f-3f88-4e17-b7dd-738b95cb117e 2013-02-05 09:57:02.845 UTC 1c82a7ea-5d2c-401b-b2e3-39a7c86a68ab 2013-01-28 15:34:16.371 UTC 5ee6b306-17f4-4522-a9cf-a4f1fcc83578 2012-06-20 14:46:27.522 UTC ab8c2488-f5c1-44c8-b5ec-719f624a8c41 2013-01-30 15:29:42.994 UTC aa90d89d-a8e4-4d82-b828-c038cf9422d1 2012-06-25 18:08:31.488 UTC 5fb7380d-11e5-4b0a-baaa-c1f6a988070b 2012-07-03 10:07:57.998 UTC dc4bff60-a506-43bb-8573-3ef97c0316d2 2012-09-12 08:11:11.792 UTC 5a01765c-980c-4476-a60b-4eebb2a7d7e4 2013-02-05 09:05:11.428 UTC 199ad955-4a64-4f3d-8afc-c4b1c2f9d08b 2012-09-04 11:17:06.46 UTC 42dc2b06-15db-4e11-8b75-3a0e1aa66e89 2012-09-12 07:16:20.526 UTC 01bdae83-abec-4364-840c-27a1224cfbd9 2012-09-07 15:02:00.202 UTC 644e2cd4-f219-4b7b-900a-a7b3f36bd9dd 2012-07-18 13:29:04.78 UTC 78a5bc98-afe7-49b5-a411-739894b618ca 2012-06-25 11:56:37.177 UTC c84310b7-61d8-4111-a9d4-1cbbc70c27f5 2012-09-11 10:01:31.727 UTC 2a2de5a5-0450-49bf-b68e-c8910124c45a 2012-06-20 13:19:11.570 UTC 438277ae-2f32-49b5-bfc1-9d92845351f2 2012-06-20 13:37:27.462 UTC f1fd209b-ec99-4713-b66b-b22e0d673f9f 2012-09-04 11:18:48.47 UTC d8ede669-0d53-4bd1-9a37-ded1cdb5bb1c 2012-06-25 12:03:27.734 UTC 0d15cb49-d14e-425b-b2c1-d1a34ce4b6f9 2013-01-28 15:14:41.764 UTC f73d30e4-44c3-4265-921c-af28f7e121ef 2012-09-11 15:01:15.447 UTC Find_co_occurring_doConceptID_111 http://rdf.biosemantics.org/owl/concept#3092619 2013-02-05 20:01:52.834 UTC Concept ID for the input concept. 2012-07-11 12:32:30.622 UTC ConceptID_211 Concept ID for the second concept. 2012-07-11 12:33:12.79 UTC http://rdf.biosemantics.org/owl/concept#4275360 2013-02-05 20:01:15.767 UTC Cutoff_value00 1 2012-07-11 12:30:25.642 UTC The number of co-occurring documents to return. 2012-07-11 12:30:11.639 UTC Document_ID 19614980 2013-02-05 19:51:47.955 UTC ID of the returned document for which the two concepts co-occur. 2013-02-05 19:51:31.314 UTC Document_title Title of the returned document for which the two concepts co-occur. 2013-02-05 19:51:24.400 UTC L-Glutamine-induced apoptosis in microglia is mediated by mitochondrial dysfunction. 2013-02-05 19:50:31.116 UTC findCoOccurringDocumentsparameters0parameters00 This Web service returns the documents in which the input concepts co-occur. A cutoff value determines the number of documents to return. 2012-09-11 12:53:06.686 UTC net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivity http://ws.biosemantics.org/ConceptRecognizerService?wsdl findCoOccurringDocuments net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 3 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokefindCoOccurringDocuments_inputconceptID10conceptID20cutoffValue0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity cutoffValue 0 'text/plain' false conceptID1 0 'text/plain' false conceptID2 0 'text/plain' false output 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="findCoOccurringDocuments" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}findCoOccurringDocuments"><s:elements><s:basetype optional="false" unbounded="false" typename="int" name="cutoffValue" qname="findCoOccurringDocuments&gt;cutoffValue" /><s:basetype optional="true" unbounded="false" typename="string" name="conceptID1" qname="findCoOccurringDocuments&gt;conceptID1" /><s:basetype optional="true" unbounded="false" typename="string" name="conceptID2" qname="findCoOccurringDocuments&gt;conceptID2" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokefindCoOccurringDocuments_outputinput0return00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false return 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="findCoOccurringDocumentsResponse" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}findCoOccurringDocumentsResponse"><s:elements><s:complextype optional="true" unbounded="false" typename="supportingDocumentsWrapper" name="return" qname="findCoOccurringDocumentsResponse&gt;return"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="cuiOwner" qname="supportingDocumentsWrapper&gt;cuiOwner" /><s:basetype optional="true" unbounded="false" typename="string" name="cuiMember" qname="supportingDocumentsWrapper&gt;cuiMember" /><s:basetype optional="true" unbounded="false" typename="int" name="originalSize" qname="supportingDocumentsWrapper&gt;originalSize" /><s:arraytype optional="true" unbounded="false" wrapped="true" typename="&gt;supportingDocumentsWrapper&gt;SupportingDocumentsList" name="SupportingDocumentsList" qname="supportingDocumentsWrapper&gt;SupportingDocumentsList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="SupportingDocument" name="" qname="{http://services.conceptrecognizer.lumc.nl/}SupportingDocument"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="title" qname="supportingDocument&gt;title" /><s:basetype optional="false" unbounded="false" typename="int" name="PMID" qname="supportingDocument&gt;PMID" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokefindCoOccurringDocuments_returninput0SupportingDocumentsList00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false cuiOwner 0 'text/plain' 0 cuiMember 0 'text/plain' 0 originalSize 0 'text/plain' 0 SupportingDocumentsList 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="true" unbounded="false" typename="supportingDocumentsWrapper" name="return" qname="findCoOccurringDocumentsResponse&gt;return"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="cuiOwner" qname="supportingDocumentsWrapper&gt;cuiOwner" /><s:basetype optional="true" unbounded="false" typename="string" name="cuiMember" qname="supportingDocumentsWrapper&gt;cuiMember" /><s:basetype optional="true" unbounded="false" typename="int" name="originalSize" qname="supportingDocumentsWrapper&gt;originalSize" /><s:arraytype optional="true" unbounded="false" wrapped="true" typename="&gt;supportingDocumentsWrapper&gt;SupportingDocumentsList" name="SupportingDocumentsList" qname="supportingDocumentsWrapper&gt;SupportingDocumentsList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="SupportingDocument" name="" qname="{http://services.conceptrecognizer.lumc.nl/}SupportingDocument"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="title" qname="supportingDocument&gt;title" /><s:basetype optional="false" unbounded="false" typename="int" name="PMID" qname="supportingDocument&gt;PMID" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokereturn_SupportingDocumentsListinput0SupportingDocumentsList11net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false SupportingDocumentsList 1 l('text/xml') 1 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:arraytype optional="true" unbounded="false" wrapped="true" typename="&gt;supportingDocumentsWrapper&gt;SupportingDocumentsList" name="SupportingDocumentsList" qname="supportingDocumentsWrapper&gt;SupportingDocumentsList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="SupportingDocument" name="" qname="{http://services.conceptrecognizer.lumc.nl/}SupportingDocument"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="title" qname="supportingDocument&gt;title" /><s:basetype optional="false" unbounded="false" typename="int" name="PMID" qname="supportingDocument&gt;PMID" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSupportingDocumentsList_SupportingDocumentsListinput0PMID00title00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false title 0 'text/plain' 0 PMID 0 'text/plain' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="SupportingDocument" name="" qname="{http://services.conceptrecognizer.lumc.nl/}SupportingDocument"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="title" qname="supportingDocument&gt;title" /><s:basetype optional="false" unbounded="false" typename="int" name="PMID" qname="supportingDocument&gt;PMID" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokefindCoOccurringDocumentsparametersfindCoOccurringDocuments_inputoutputfindCoOccurringDocuments_inputconceptID1ConceptID_1findCoOccurringDocuments_inputconceptID2ConceptID_2findCoOccurringDocuments_inputcutoffValueCutoff_valuefindCoOccurringDocuments_outputinputfindCoOccurringDocumentsparametersfindCoOccurringDocuments_returninputfindCoOccurringDocuments_outputreturnreturn_SupportingDocumentsListinputfindCoOccurringDocuments_returnSupportingDocumentsListSupportingDocumentsList_SupportingDocumentsListinputreturn_SupportingDocumentsListSupportingDocumentsListDocument_IDSupportingDocumentsList_SupportingDocumentsListPMIDDocument_titleSupportingDocumentsList_SupportingDocumentsListtitle ab19809c-64de-48aa-b573-563d94dd784c 2012-07-11 12:34:09.767 UTC e609f005-94e4-4f8c-b796-50f567459a97 2013-02-05 20:01:53.20 UTC a40a52c8-90c5-4755-a6c5-acae5f99b0e6 2012-09-11 12:53:08.81 UTC Find co-occurring documents 2012-07-11 12:35:28.748 UTC 234b78c5-66c4-4e83-bbe0-a21ec539a50d 2012-07-18 13:24:34.655 UTC 58b2cab3-cf9d-419f-b41a-241990b5bc21 2013-02-05 19:51:48.145 UTC 739b02c1-fc07-41e3-b4e5-9a7174e4df7a 2013-02-04 10:58:13.386 UTC 856c7313-b7d7-4522-a152-bf4f5bf5830d 2013-02-04 14:13:02.886 UTC Creator: Kristina Hettne Contributors: Web services by Reinout van Schouwen Additional annotations by Marco Roos 2012-07-18 13:23:59.195 UTC d42b0294-a5cf-4cfc-9635-26486e613934 2012-09-04 11:17:59.103 UTC 3beae759-c94b-45ff-99ab-d5471960ec11 2013-02-04 14:11:28.416 UTC 6c42e1a2-7aec-4169-a712-79b6cf072937 2012-07-11 12:36:19.218 UTC Purpose: This workflow search an indexed literature database for documents mentioning both of the input concepts. Author 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 13:24:29.315 UTC 324bd118-08c0-4cc2-a3cf-86a0a6d802e0 2012-07-11 12:39:06.872 UTC Get_concept_informatConcept_ID00 http://rdf.biosemantics.org/owl/concept#3092619 2013-02-05 19:57:02.768 UTC Concept ID of the concept to retrieve the name for. 2013-02-05 20:06:06.218 UTC Concept_name The name of the concept. 2012-07-04 11:51:39.675 UTC GLS2 2012-07-04 11:55:50.464 UTC Concept_ID http://rdf.biosemantics.org/owl/concept#3092619 2013-02-05 19:56:21.234 UTC getConceptProfileparameters0parameters00 This Web service returns the concept profile for a given concept ID. 2012-09-11 12:51:04.847 UTC net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivity http://ws.biosemantics.org/ConceptRecognizerService?wsdl getConceptProfile net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetConceptProfile_inputconceptId0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity conceptId 0 'text/plain' false output 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getConceptProfile" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}getConceptProfile"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptId" qname="getConceptProfile&gt;conceptId" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetConceptProfile_outputinput0return00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false return 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getConceptProfileResponse" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}getConceptProfileResponse"><s:elements><s:complextype optional="true" unbounded="false" typename="conceptProfileWrapper" name="return" qname="getConceptProfileResponse&gt;return"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptId" qname="conceptProfileWrapper&gt;conceptId" /><s:basetype optional="true" unbounded="false" typename="string" name="name" qname="conceptProfileWrapper&gt;name" /><s:basetype optional="true" unbounded="false" typename="string" name="definition" qname="conceptProfileWrapper&gt;definition" /><s:arraytype optional="true" unbounded="false" wrapped="true" typename="&gt;conceptProfileWrapper&gt;ConceptVector" name="ConceptVector" qname="conceptProfileWrapper&gt;ConceptVector"><s:elementtype><s:complextype optional="false" unbounded="false" typename="stringDoubleTuple" name="" qname="{http://services.conceptrecognizer.lumc.nl/}stringDoubleTuple"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="queryConceptID" qname="stringDoubleTuple&gt;queryConceptID" /><s:basetype optional="true" unbounded="false" typename="double" name="score" qname="stringDoubleTuple&gt;score" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetConceptProfile_returninput0conceptId00name00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false conceptId 0 'text/plain' 0 name 0 'text/plain' 0 definition 0 'text/plain' 0 ConceptVector 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="true" unbounded="false" typename="conceptProfileWrapper" name="return" qname="getConceptProfileResponse&gt;return"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptId" qname="conceptProfileWrapper&gt;conceptId" /><s:basetype optional="true" unbounded="false" typename="string" name="name" qname="conceptProfileWrapper&gt;name" /><s:basetype optional="true" unbounded="false" typename="string" name="definition" qname="conceptProfileWrapper&gt;definition" /><s:arraytype optional="true" unbounded="false" wrapped="true" typename="&gt;conceptProfileWrapper&gt;ConceptVector" name="ConceptVector" qname="conceptProfileWrapper&gt;ConceptVector"><s:elementtype><s:complextype optional="false" unbounded="false" typename="stringDoubleTuple" name="" qname="{http://services.conceptrecognizer.lumc.nl/}stringDoubleTuple"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="queryConceptID" qname="stringDoubleTuple&gt;queryConceptID" /><s:basetype optional="true" unbounded="false" typename="double" name="score" qname="stringDoubleTuple&gt;score" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetConceptProfileparametersgetConceptProfile_inputoutputgetConceptProfile_inputconceptIdConcept_IDgetConceptProfile_outputinputgetConceptProfileparametersgetConceptProfile_returninputgetConceptProfile_outputreturnConcept_namegetConceptProfile_returnnameConcept_IDgetConceptProfile_returnconceptId 3afe257a-1246-4267-be82-ccb4203af53f 2013-02-04 14:49:02.214 UTC 0f9f0834-7609-4af4-b3dd-6a9452cda123 2012-09-11 12:44:40.991 UTC Get concept information 2012-07-04 11:53:15.951 UTC 4b5150df-f12d-4f9a-a51e-a655e4c3cba1 2013-02-04 14:41:45.41 UTC The workflow takes a concept ID as input and returns the ID, definition and name of the concept. This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery. 2012-07-18 13:22:23.330 UTC Creator: Kristina Hettne on behalf of the BioSemantics group Contributions: Web services by Reinout van Schouwen 2012-07-18 13:22:40.527 UTC 80bc71ed-b511-4824-98e2-3e5add19aaae 2012-09-07 14:29:24.729 UTC cefac9de-143f-47d7-b318-2af786d92046 2013-02-04 14:52:58.669 UTC c6eaa639-5ee7-474e-9dbb-401927d65030 2012-09-11 12:49:35.323 UTC cf644a3e-3942-4c42-b8c7-2f834fd110d4 2012-07-18 13:22:54.983 UTC 2824bc65-af91-41c0-8912-e24151314a57 2012-09-11 12:51:06.419 UTC d9f930cb-1c79-46de-9935-e97cc62f5df7 2013-02-05 19:57:02.921 UTC b31a4602-eda2-485b-ad82-07db5fe82068 2012-07-04 11:54:39.48 UTC ff59aa50-8acd-40d6-b6dc-042b289db314 2013-02-05 11:10:08.41 UTC a2ecda87-b5b6-473a-af29-b9fcf32ea707 2012-09-11 12:40:55.902 UTC dea60608-70c7-4cf0-a8da-8513eb1a440a 2012-09-04 11:17:36.783 UTC 04d2b539-0ecf-47a2-b036-73e97581556f 2012-07-04 11:56:13.312 UTC 83c3dad7-8d79-44e4-959a-e01ab677a645 2013-02-05 20:06:08.228 UTC Explain_concept_scoresC_ConceptID00 The concept id of the C concept. 2012-09-11 09:01:25.824 UTC http://rdf.biosemantics.org/owl/concept#2263126 2013-02-05 20:09:11.301 UTC cutoff00 Maximum number of explanatory concepts to return. 2012-09-11 08:30:14.173 UTC 1 2012-09-10 15:18:30.889 UTC A_ConceptID00 The concept id of the A concept. 2012-09-11 09:01:33.736 UTC http://rdf.biosemantics.org/owl/concept#3096431 2013-02-05 20:09:19.271 UTC B_ConceptName FADS2 2012-09-10 15:17:05.627 UTC The concept name of the explanatory B concept. 2012-09-11 09:01:44.136 UTC B_ConceptID http://rdf.biosemantics.org/owl/concept#3096431 2013-02-05 20:09:37.980 UTC The concept ID of the explanatory B concept. 2012-09-11 09:01:40.385 UTC B_ConceptContribution 43.36232841014862 2012-09-10 15:16:19.600 UTC The contribution score, that is, the percentage of the contributions of the individual concepts to the coherence score (the average of the inner product scores of all possible concept pairs within the group). 2012-09-11 08:58:01.819 UTC explainScoresStringInputparameters0parameters00 This Web service takes two concept ids as input and returns the top ranking "B" concepts according to Swanson's ABC model of discovery, where the relationships AB and BC are known and reported in the literature, and the implicit relationship AC is a putative new discovery. It might also be the case that AC is already known. In that case AC does not represent a new discovery but will still be returned by the Web service. The concept contribution is also reported by the Web service. The concept contribution is the percentage of the contributions of the individual concepts to the coherence score (the average of the inner product scores of all possible concept pairs within the group). 2012-09-11 08:57:10.939 UTC net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivity http://ws.biosemantics.org/ConceptRecognizerService?wsdl explainScoresStringInput net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeexplainScoresStringInput_inputcutoffValue0conceptCUIsAsString0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity cutoffValue 0 'text/plain' false conceptCUIsAsString 0 'text/plain' false output 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="explainScoresStringInput" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}explainScoresStringInput"><s:elements><s:basetype optional="false" unbounded="false" typename="int" name="cutoffValue" qname="explainScoresStringInput&gt;cutoffValue" /><s:basetype optional="true" unbounded="false" typename="string" name="conceptCUIsAsString" qname="explainScoresStringInput&gt;conceptCUIsAsString" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeexplainScoresStringInput_outputinput0return00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false return 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="explainScoresStringInputResponse" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}explainScoresStringInputResponse"><s:elements><s:complextype optional="true" unbounded="false" typename="conceptContributionsWrapper" name="return" qname="explainScoresStringInputResponse&gt;return"><s:elements><s:arraytype optional="true" unbounded="false" wrapped="true" typename="&gt;conceptContributionsWrapper&gt;ConceptContributionTable" name="ConceptContributionTable" qname="conceptContributionsWrapper&gt;ConceptContributionTable"><s:elementtype><s:complextype optional="false" unbounded="false" typename="conceptContribution" name="" qname="{http://services.conceptrecognizer.lumc.nl/}conceptContribution"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptName" qname="conceptContribution&gt;conceptName" /><s:basetype optional="true" unbounded="false" typename="double" name="contribution" qname="conceptContribution&gt;contribution" /><s:basetype optional="true" unbounded="false" typename="int" name="conceptId" qname="conceptContribution&gt;conceptId" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeexplainScoresStringInput_returninput0ConceptContributionTable00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false ConceptContributionTable 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="true" unbounded="false" typename="conceptContributionsWrapper" name="return" qname="explainScoresStringInputResponse&gt;return"><s:elements><s:arraytype optional="true" unbounded="false" wrapped="true" typename="&gt;conceptContributionsWrapper&gt;ConceptContributionTable" name="ConceptContributionTable" qname="conceptContributionsWrapper&gt;ConceptContributionTable"><s:elementtype><s:complextype optional="false" unbounded="false" typename="conceptContribution" name="" qname="{http://services.conceptrecognizer.lumc.nl/}conceptContribution"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptName" qname="conceptContribution&gt;conceptName" /><s:basetype optional="true" unbounded="false" typename="double" name="contribution" qname="conceptContribution&gt;contribution" /><s:basetype optional="true" unbounded="false" typename="int" name="conceptId" qname="conceptContribution&gt;conceptId" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokereturn_ConceptContributionTable_2input0ConceptContributionTable11net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false ConceptContributionTable 1 l('text/xml') 1 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:arraytype optional="true" unbounded="false" wrapped="true" typename="&gt;conceptContributionsWrapper&gt;ConceptContributionTable" name="ConceptContributionTable" qname="conceptContributionsWrapper&gt;ConceptContributionTable"><s:elementtype><s:complextype optional="false" unbounded="false" typename="conceptContribution" name="" qname="{http://services.conceptrecognizer.lumc.nl/}conceptContribution"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptName" qname="conceptContribution&gt;conceptName" /><s:basetype optional="true" unbounded="false" typename="double" name="contribution" qname="conceptContribution&gt;contribution" /><s:basetype optional="true" unbounded="false" typename="int" name="conceptId" qname="conceptContribution&gt;conceptId" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke2_ConceptContributionTableinput0contribution00conceptId00conceptName00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false conceptName 0 'text/plain' 0 contribution 0 'text/plain' 0 conceptId 0 'text/plain' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="conceptContribution" name="" qname="{http://services.conceptrecognizer.lumc.nl/}conceptContribution"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptName" qname="conceptContribution&gt;conceptName" /><s:basetype optional="true" unbounded="false" typename="double" name="contribution" qname="conceptContribution&gt;contribution" /><s:basetype optional="true" unbounded="false" typename="int" name="conceptId" qname="conceptContribution&gt;conceptId" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemakeCommaSeparatedStringitem20item10output00 This script concatenates the two input concept id strings and adds a comma in between. 2012-09-11 08:29:47.911 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity item1 0 text/plain java.lang.String true item2 0 text/plain java.lang.String true output 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeexplainScoresStringInputparametersexplainScoresStringInput_inputoutputexplainScoresStringInput_inputcutoffValuecutoffexplainScoresStringInput_inputconceptCUIsAsStringmakeCommaSeparatedStringoutputexplainScoresStringInput_outputinputexplainScoresStringInputparametersexplainScoresStringInput_returninputexplainScoresStringInput_outputreturnreturn_ConceptContributionTable_2inputexplainScoresStringInput_returnConceptContributionTable2_ConceptContributionTableinputreturn_ConceptContributionTable_2ConceptContributionTablemakeCommaSeparatedStringitem2C_ConceptIDmakeCommaSeparatedStringitem1A_ConceptIDB_ConceptName2_ConceptContributionTableconceptNameB_ConceptID2_ConceptContributionTableconceptIdB_ConceptContribution2_ConceptContributionTablecontribution Purpose of workflow: This workflow takes two concept ids as input and returns the top ranking "B" concepts according to Swanson's ABC model of discovery, where the relationships AB and BC are known and reported in the literature, and the implicit relationship AC is a putative new discovery. It might also be the case that AC is already known. In that case AC does not represent a new discovery but will still be returned (see workflow example values). The B concepts are returned sorted on the percentage of the contributions of the individual concepts to the coherence score (the average of the inner product scores of all possible concept pairs within the group). This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery. 2012-09-11 09:11:13.758 UTC 89f2da6a-161b-47b1-a048-a65fd35f912c 2012-01-06 11:47:16.46 UTC 8efd062c-22d8-4fc6-bfe4-ea8f96ba7e2a 2012-04-16 12:58:21.8 UTC 7a995f89-0c37-48b9-b0f7-8eca5cd36420 2012-01-06 11:51:06.790 UTC 4bed166d-9815-4a35-a613-869b300b7973 2012-04-16 13:04:34.678 UTC 13050a9d-bdda-4de5-8bc7-8503457302cd 2012-04-16 13:02:36.340 UTC 8d4a9091-0ba9-468e-9883-7b08e5212cd2 2012-04-16 13:07:32.864 UTC 7d6ba6db-2552-4c15-b800-1789f5385d44 2012-09-07 15:18:14.352 UTC 90f0af1e-a653-4a85-889c-4120accdd9d9 2012-09-07 14:44:36.440 UTC abaeb048-e186-4c8d-92d4-6b32b22603d8 2012-04-16 13:01:16.427 UTC 3c6eca00-e3a8-46b8-86bd-7c4b48a3ac77 2012-07-18 13:20:01.872 UTC fc7ae322-fcac-41c5-b136-0767d52680b0 2012-03-21 13:53:26.66 UTC Explain concept scores 2012-04-16 13:00:42.27 UTC 4b937a61-6180-48ce-a679-cf3ed1c8f208 2012-09-11 08:58:54.136 UTC 4f826cfe-3950-4151-bbe6-bff67413be51 2012-09-07 15:22:15.103 UTC Creator: Reinout van Schouwen on behalf of the BIoSemantics Group Adaptations by Marco Roos and Kristina Hettne 2012-09-11 09:02:52.112 UTC 713fa342-cdf4-48b7-850d-abecb37b9b1f 2012-09-11 08:58:13.328 UTC a6c096b8-050d-48bf-8b9c-114762aac26d 2012-09-07 14:52:03.90 UTC 2b762f5e-4473-4d48-b78f-df306600467a 2012-09-11 09:11:13.838 UTC 6bab82da-54d0-4bc7-96fd-e5c5d3c6d77f 2012-09-07 14:37:53.808 UTC 88e1d0d3-3377-4a21-a98f-19020444e686 2012-09-07 14:58:20.922 UTC 0faa8a91-3a1c-4e03-b74d-f271e7b96290 2012-04-16 12:55:56.499 UTC 9e4c2fcc-6dcc-46d5-9edd-d7841389ef5c 2012-04-17 08:22:27.551 UTC 9a6508bd-87c3-4d9c-99f2-9003b5b57df4 2012-09-11 09:01:50.31 UTC 1ea652c5-572b-4b0a-b66d-5ae41a7b7fe1 2013-02-05 09:41:27.678 UTC a260c127-7bbc-4dde-86a9-80647fcbb862 2012-09-10 15:18:42.957 UTC 09802e77-93ac-45ba-9ad5-e7bea33cda8b 2013-02-05 20:09:38.174 UTC 2b5167d3-3864-46c1-b761-b66ab721da54 2012-02-03 13:52:44.748 UTC 541a7a2d-e3e3-490d-885b-52d653a21d11 2012-02-03 11:42:15.89 UTC bb8d1d77-e3d2-4cee-aee9-3cd4e1bd8547 2012-01-06 12:38:00.681 UTC c416805f-aa9d-4d44-b434-f253935ed0ef 2012-09-11 08:57:11.33 UTC 8f284446-2578-4c4d-b81d-e842a463641b 2012-09-07 15:34:00.455 UTC 142a2c6d-8e96-4c9f-ad64-da97fd4c2597 2012-09-04 11:16:44.759 UTC Get_concept_informatConcept_ID00 http://rdf.biosemantics.org/owl/concept#3092619 2013-02-05 20:07:38.791 UTC Concept ID of the concept to retrieve name and definition for. 2012-07-04 11:50:31.405 UTC Concept_name The name of the concept. 2012-07-04 11:51:39.675 UTC GLS2 2012-07-04 11:55:50.464 UTC getConceptProfileparameters0parameters00 This Web service returns the concept profile for a given concept ID. 2012-09-11 12:51:04.847 UTC net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivity http://ws.biosemantics.org/ConceptRecognizerService?wsdl getConceptProfile net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetConceptProfile_inputconceptId0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity conceptId 0 'text/plain' false output 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getConceptProfile" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}getConceptProfile"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptId" qname="getConceptProfile&gt;conceptId" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetConceptProfile_outputinput0return00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false return 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getConceptProfileResponse" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}getConceptProfileResponse"><s:elements><s:complextype optional="true" unbounded="false" typename="conceptProfileWrapper" name="return" qname="getConceptProfileResponse&gt;return"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptId" qname="conceptProfileWrapper&gt;conceptId" /><s:basetype optional="true" unbounded="false" typename="string" name="name" qname="conceptProfileWrapper&gt;name" /><s:basetype optional="true" unbounded="false" typename="string" name="definition" qname="conceptProfileWrapper&gt;definition" /><s:arraytype optional="true" unbounded="false" wrapped="true" typename="&gt;conceptProfileWrapper&gt;ConceptVector" name="ConceptVector" qname="conceptProfileWrapper&gt;ConceptVector"><s:elementtype><s:complextype optional="false" unbounded="false" typename="stringDoubleTuple" name="" qname="{http://services.conceptrecognizer.lumc.nl/}stringDoubleTuple"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="queryConceptID" qname="stringDoubleTuple&gt;queryConceptID" /><s:basetype optional="true" unbounded="false" typename="double" name="score" qname="stringDoubleTuple&gt;score" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetConceptProfile_returninput0name00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false conceptId 0 'text/plain' 0 name 0 'text/plain' 0 definition 0 'text/plain' 0 ConceptVector 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="true" unbounded="false" typename="conceptProfileWrapper" name="return" qname="getConceptProfileResponse&gt;return"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptId" qname="conceptProfileWrapper&gt;conceptId" /><s:basetype optional="true" unbounded="false" typename="string" name="name" qname="conceptProfileWrapper&gt;name" /><s:basetype optional="true" unbounded="false" typename="string" name="definition" qname="conceptProfileWrapper&gt;definition" /><s:arraytype optional="true" unbounded="false" wrapped="true" typename="&gt;conceptProfileWrapper&gt;ConceptVector" name="ConceptVector" qname="conceptProfileWrapper&gt;ConceptVector"><s:elementtype><s:complextype optional="false" unbounded="false" typename="stringDoubleTuple" name="" qname="{http://services.conceptrecognizer.lumc.nl/}stringDoubleTuple"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="queryConceptID" qname="stringDoubleTuple&gt;queryConceptID" /><s:basetype optional="true" unbounded="false" typename="double" name="score" qname="stringDoubleTuple&gt;score" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetConceptProfileparametersgetConceptProfile_inputoutputgetConceptProfile_inputconceptIdConcept_IDgetConceptProfile_outputinputgetConceptProfileparametersgetConceptProfile_returninputgetConceptProfile_outputreturnConcept_namegetConceptProfile_returnname 3afe257a-1246-4267-be82-ccb4203af53f 2013-02-04 14:49:02.214 UTC b31a4602-eda2-485b-ad82-07db5fe82068 2012-07-04 11:54:39.48 UTC 04d2b539-0ecf-47a2-b036-73e97581556f 2012-07-04 11:56:13.312 UTC 80bc71ed-b511-4824-98e2-3e5add19aaae 2012-09-07 14:29:24.729 UTC dea60608-70c7-4cf0-a8da-8513eb1a440a 2012-09-04 11:17:36.783 UTC cf644a3e-3942-4c42-b8c7-2f834fd110d4 2012-07-18 13:22:54.983 UTC Creator: Kristina Hettne on behalf of the BioSemantics group Contributions: Web services by Reinout van Schouwen 2012-07-18 13:22:40.527 UTC 2824bc65-af91-41c0-8912-e24151314a57 2012-09-11 12:51:06.419 UTC The workflow takes a concept ID as input and returns the ID, definition and name of the concept. This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery. 2012-07-18 13:22:23.330 UTC Get concept information 2012-07-04 11:53:15.951 UTC a2ecda87-b5b6-473a-af29-b9fcf32ea707 2012-09-11 12:40:55.902 UTC 0f9f0834-7609-4af4-b3dd-6a9452cda123 2012-09-11 12:44:40.991 UTC 6a41503c-d915-4eac-998e-0d10ee8f32f1 2013-02-05 20:07:44.871 UTC c6eaa639-5ee7-474e-9dbb-401927d65030 2012-09-11 12:49:35.323 UTC 4b5150df-f12d-4f9a-a51e-a655e4c3cba1 2013-02-04 14:41:45.41 UTC SNP_ID2EntrezGene_IDSNP_ID00 rs2657879 2012-07-16 14:27:52.745 UTC Use (a list of) Database of Single Nucleotide Polymorphisms (dbSNP) IDs as input, separated by the newline character (\n). 2012-07-16 14:27:32.982 UTC set_width00 The allows the user to set the flanking width for the gene for determining SNPs. 2012-09-11 11:08:34.646 UTC 100000 2012-09-11 11:08:43.702 UTC EntrezGene_ID 8914 4284 283377 27165 2012-07-16 14:30:19.975 UTC A list of EntrezGene IDs. 2012-07-16 14:29:53.708 UTC extract_snp_idstring0out100 This extracts the contents (snp_ids) from the input. 2012-09-11 10:15:10.813 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity string 0 text/plain java.lang.String true out1 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSplit_string_into_string_list_by_regular_expressionregex0string0split11 This service splits the string value into a string list at every occurrence of the specified regular expression. The regular expression provided in this case is a new line: "\n" 2012-09-11 11:06:15.406 UTC net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity string 0 'text/plain' java.lang.String true regex 0 'text/plain' java.lang.String true split 1 l('text/plain') 1 workflow org.embl.ebi.escience.scuflworkers.java.SplitByRegex net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregex_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity \n net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokehsapiens_snphsapiens_snp.snp_filter_filter0hsapiens_snp.chrom_start10hsapiens_snp.chr_name10 This is a Biomart service that takes the SNP ID as the input and returns chromosome name, and the position of the SNP. 2012-09-11 11:06:51.62 UTC net.sf.taverna.t2.activitiesbiomart-activity1.4net.sf.taverna.t2.activities.biomart.BiomartActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_Listinputlist2outputlist11 This service flattens the inputlist by one level. It returns the result of the flattening. 2012-09-11 11:07:13.494 UTC net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity inputlist 2 l(l('')) [B true outputlist 1 l('') 1 workflow org.embl.ebi.escience.scuflworkers.java.FlattenList net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_List_2inputlist2outputlist11 This service flattens the inputlist by one level. It returns the result of the flattening. 2012-09-11 11:07:17.605 UTC net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity inputlist 2 l(l('')) [B true outputlist 1 l('') 1 workflow org.embl.ebi.escience.scuflworkers.java.FlattenList net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeinput_chr_positionchr_in1in21in11chr_out11end_out11start_out11 The purpose of this beanshell is to manipulate the start and end positions based on the flanking width provided by the user. 2012-09-11 11:07:41.333 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity chr_in 1 text/plain java.lang.String true in2 1 text/plain java.lang.String true in1 1 text/plain java.lang.String true chr_out 1 1 end_out 1 1 start_out 1 1 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokehsapiens_gene_ensemblhsapiens_gene_ensembl.chromosome_name_filter0hsapiens_gene_ensembl.end_filter0hsapiens_gene_ensembl.start_filter0hsapiens_gene_ensembl.entrezgene10 This is a Biomart service that takes the chromosome name and start and end positions and returns genes (entrez gene id) present in the region. 2012-09-11 11:09:54.820 UTC net.sf.taverna.t2.activitiesbiomart-activity1.4net.sf.taverna.t2.activities.biomart.BiomartActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeextract_snp_idstringSplit_string_into_string_list_by_regular_expressionsplitSplit_string_into_string_list_by_regular_expressionregexregex_valuevalueSplit_string_into_string_list_by_regular_expressionstringSNP_IDhsapiens_snphsapiens_snp.snp_filter_filterextract_snp_idout1Flatten_Listinputlisthsapiens_snphsapiens_snp.chr_nameFlatten_List_2inputlisthsapiens_snphsapiens_snp.chrom_startinput_chr_positionchr_inFlatten_Listoutputlistinput_chr_positionin2Flatten_List_2outputlistinput_chr_positionin1set_widthhsapiens_gene_ensemblhsapiens_gene_ensembl.chromosome_name_filterinput_chr_positionchr_outhsapiens_gene_ensemblhsapiens_gene_ensembl.end_filterinput_chr_positionend_outhsapiens_gene_ensemblhsapiens_gene_ensembl.start_filterinput_chr_positionstart_outEntrezGene_IDhsapiens_gene_ensemblhsapiens_gene_ensembl.entrezgene e7471436-942d-4d3e-98b2-65e15995183e 2012-05-28 16:15:51.854 UTC 1e2fc50e-6f54-4c4b-854c-aecf80d24272 2012-05-23 09:11:52.877 UTC 4c1c8924-c2c3-4410-bf73-5db2e4435998 2012-07-09 14:51:20.747 UTC 59c48ad2-46fa-4c6a-920e-35585a726e7f 2012-07-13 12:50:51.21 UTC 821e379f-0aaf-4220-8d6c-83517950317f 2012-05-25 15:10:34.774 UTC 537f3d64-b1fd-43bd-9c13-ad4372dd7a51 2012-05-29 09:49:35.836 UTC 8c5e8e26-1959-47e8-931a-f3d605354524 2011-12-04 20:25:27.361 UTC a8ff4a9e-1161-41d9-b903-4d1fd1fd25e4 2012-05-29 09:13:08.665 UTC 9d84acd8-2d53-46c1-b1d0-d395b26d5ffc 2012-05-25 14:14:15.364 UTC 892ce0b4-fffd-4962-a850-445e2afe54c9 2012-05-28 14:26:47.563 UTC 9916b6e6-526d-4583-b390-64518c4f06a1 2012-07-13 03:37:35.435 UTC 720aa582-de73-463d-b2bc-ddd1699ebc4b 2012-05-24 06:55:01.111 UTC 37852792-3988-4ca1-894b-f18c3e6caa3d 2012-05-28 13:36:48.449 UTC 909dac87-86fa-4b27-b8f0-e58b6acf0329 2011-12-02 20:03:51.11 UTC 470b1948-bcb8-401e-88ee-72172c9a1c75 2012-05-25 14:15:48.972 UTC 56ab1507-d44d-4569-b627-7984fe3da0aa 2011-12-05 08:55:56.457 UTC 6dc63288-570b-4c6f-9d1b-3018852941bf 2012-05-24 14:32:15.752 UTC 0d757f59-9497-426a-b0dd-bdb68d3796d0 2012-05-24 11:52:38.509 UTC 98b01cc5-cc3c-4a1b-b6bb-cc4e69c05340 2011-12-05 12:35:10.779 UTC 07f68d25-cfa2-431a-a66f-7f30ffbef86c 2012-05-29 07:46:27.651 UTC 7732d491-9163-41d3-b43e-07f5e3710a5b 2012-07-13 03:45:40.363 UTC f02a8cf2-7757-4252-b5ac-ad6729f9d80f 2011-12-05 08:51:49.367 UTC de5376be-26df-4424-82f6-735797ecbb4d 2011-12-04 19:54:39.289 UTC d7cc4df4-9383-4543-870f-1beaa09c70f7 2012-05-29 10:05:40.594 UTC 681bb15e-0cb0-4d46-b94d-50c8af23d582 2011-12-05 10:05:00.123 UTC 0fe8a23c-ab84-4025-a5c0-27c652d9b7eb 2012-05-28 15:06:02.685 UTC 57237b54-36f7-4a2c-9833-4ab73bf3cea9 2011-12-02 20:06:32.660 UTC 65969e5e-369b-46b3-88d7-22747d38898a 2012-05-29 09:14:34.991 UTC c6a4b654-7519-49bf-bb26-82fd81e32d52 2012-05-28 14:47:56.177 UTC aa1e05f9-bef7-4a1e-9137-f9a139fc6328 2012-05-28 16:17:11.384 UTC 9052cca1-3bac-456e-8964-bc5a97f24e12 2012-05-23 09:47:46.18 UTC b997e938-3b2d-4ac3-a0ec-b90fa5ecfb86 2012-05-24 07:56:27.406 UTC 1f56ace0-7a91-4cdb-80d2-078c96175c7a 2012-05-24 07:59:59.475 UTC 27f67a96-5a0f-4b9f-bc36-e487b3022324 2011-12-05 10:09:35.932 UTC 63150755-7e2c-46fa-9b18-d0af094e6bdb 2012-07-13 11:16:52.800 UTC caeeda28-d63a-4967-86a1-60b9f82afdbc 2012-07-13 11:40:22.904 UTC 4e8abbc2-c7d4-4763-a86a-b9238bc71a0a 2012-05-23 09:46:24.941 UTC 6327f30f-f86f-407f-b65b-25dc8dd3a022 2012-05-28 15:28:42.515 UTC 661bc095-4dce-4ec9-885a-62cd4678a17d 2012-05-25 15:39:45.220 UTC 131530e7-7bf2-440b-8ae4-7de74e470426 2012-05-28 14:56:56.476 UTC a8101120-66aa-437d-9f54-7c75e8bcb4c6 2012-05-29 09:41:06.977 UTC 9ffd5551-67e7-42d9-b857-a449592ca31a 2012-07-13 11:48:52.784 UTC c5edb75b-4a94-4aa8-80a7-05d514432719 2011-12-05 12:41:04.327 UTC 7984a5dc-f5ce-4991-aac7-0f4e76134197 2011-12-04 20:31:49.46 UTC fe2b3810-d054-405f-8693-866dde2fcc60 2012-05-24 10:26:45.775 UTC 761dc8af-f42e-47b0-a69b-b68ee156be89 2012-05-24 11:35:02.275 UTC fcbc52b2-3f39-41cf-9eb2-f17badb0827c 2012-05-29 09:25:28.151 UTC 4a0bd72f-205f-4fe2-aabf-4811716d04a3 2012-05-28 15:35:32.913 UTC 73ef94bb-6b99-402a-9305-e57e5ce4f5dc 2012-07-13 10:41:55.216 UTC f4ba5bba-e195-456c-9fce-4c7a04ef8e23 2012-05-28 13:11:04.53 UTC d9d5b914-c845-47f6-baa5-4965149a3eb6 2012-05-28 13:14:24.783 UTC d7ddba62-2e21-4c6d-aaba-6bd5600af8b0 2012-05-29 09:45:01.263 UTC 20b3043a-15dc-4c96-a5aa-9fb1a5ade917 2011-12-05 13:10:38.566 UTC aa8a665b-2e33-4b91-b596-c3b36cd8b714 2012-05-29 09:54:53.96 UTC d17e3593-215f-4c1d-8289-1111c4048036 2012-09-04 09:41:42.976 UTC 31edde4d-c021-4050-8192-3547f650035e 2012-05-28 13:16:38.232 UTC 780ac0b7-a424-49aa-9a7f-deb714fb52a6 2012-05-28 13:48:07.271 UTC f070ba04-399b-4422-94e9-7ac859c74e0a 2012-05-28 14:48:31.535 UTC 66d2a846-2d42-40a1-ac4a-0cb5ece59b2b 2012-07-13 19:44:04.313 UTC e70800df-db56-46cc-95c6-7331be9cfc22 2012-05-25 14:43:01.545 UTC 16c48a91-f694-48c0-9554-2e4694e04c61 2012-05-24 14:42:37.630 UTC 86c1c5b0-b948-4ef3-842e-ed08c6b9f6d9 2011-12-05 09:46:35.437 UTC 489c0706-b993-44cc-878e-02cd52c0757a 2012-05-28 13:28:40.258 UTC 7ffb408f-a8d9-4937-a761-0de05f695aee 2012-05-28 13:15:23.516 UTC 4717b80f-c414-4cef-a833-5c7434445481 2011-12-04 20:17:49.522 UTC 0550476f-da31-4066-b14f-f5f483f232fa 2012-05-28 13:12:01.864 UTC 49cf34cf-c5c0-4623-bf73-4a16d0750f9c 2012-07-12 23:18:21.867 UTC fc7d0b18-95da-435a-a49c-bd4957d01929 2012-05-28 13:22:58.144 UTC a3dc86e8-ceb9-4224-a702-83ef11cddaa1 2011-12-02 20:12:19.143 UTC c65a9a3a-909c-42a3-83cf-edd32d2e7aa9 2012-05-23 09:39:51.321 UTC df724031-6ef9-4bbf-80d1-0978f512f166 2012-05-24 07:13:09.787 UTC 400ed11a-24fd-457a-a9b7-cc3ef85e8ad7 2012-05-24 11:44:12.16 UTC d22656b0-2793-4ba7-8f90-1f80c27d5413 2012-07-10 12:46:34.516 UTC bb845add-ef95-4621-ba20-7cdbcfd8895c 2012-05-28 14:30:06.480 UTC 323b72ad-2dad-491c-adcc-4b01f61d15c5 2012-07-13 03:48:12.471 UTC 6d2380e8-5477-48e8-9ed1-c82d71a347fc 2012-05-24 11:32:30.203 UTC 45f3551e-d015-4ca6-b0df-e1607fa965b0 2012-05-28 14:22:00.164 UTC 773ad5ff-fa77-4807-9699-bc75f0be63b9 2011-12-04 19:55:52.32 UTC 3e9f3842-9dfc-4b71-a356-a1516667a065 2012-05-28 16:29:16.964 UTC 663775b4-68ba-4dfe-8aa3-2a079a61805c 2012-05-28 13:17:48.527 UTC 799b2c7a-749d-4e85-96b8-57d4ce9d49a8 2012-05-28 13:49:09.988 UTC c98b52f2-07a9-41c1-93e2-537baaca690f 2012-05-25 14:45:00.606 UTC 1f9fa403-1de0-4605-ae95-7964bb2b2a91 2012-05-23 09:00:46.292 UTC 2082c444-8dc5-491d-98f0-a38e48f14ad2 2012-05-28 14:58:09.975 UTC bd87bc54-b86c-48c1-9bcc-0d943cad671e 2011-12-02 19:52:46.244 UTC 5b0b16b2-6159-4a45-8f0e-e61e52a42ed0 2011-12-05 12:50:24.222 UTC 63da0a3f-eb7a-4b96-a50f-476d09f0f6b8 2012-05-24 10:14:07.658 UTC 8481be24-7358-4c81-a8fc-2b2b89f0069e 2012-07-14 03:17:33.803 UTC 122b2bb9-fdc0-4545-a673-487ec8eb4c9f 2012-05-28 13:32:55.580 UTC e2cf19ae-7516-4842-9c8d-7243da52e6fd 2012-05-28 13:23:25.66 UTC 594f53e9-a4fd-422b-b11a-c95aeae12f6b 2012-05-25 14:18:14.345 UTC 3105f50e-deab-4464-8ac2-ab81746a8e1a 2012-05-28 15:01:00.409 UTC 5d768f1f-89a3-4e49-8852-f00f1870d335 2012-07-18 13:09:23.517 UTC c14f091a-a1b6-43a6-af28-7599b1ddd8b1 2012-05-24 07:08:23.312 UTC 2ce8d6ce-78ef-4ba3-93f3-ae418cb04a04 2012-05-24 11:37:44.705 UTC f6370d45-5817-4828-98e5-8fa459e52876 2012-05-28 13:30:49.145 UTC 33f3d4e3-80a9-44ec-8cfb-f84ebc21051c 2012-05-28 12:44:30.573 UTC 78067d1f-1fb1-404d-9494-50154802f9d9 2012-07-09 14:24:55.244 UTC 07448a4e-6711-403d-80a7-bbce3a10c9e5 2012-05-23 10:24:50.354 UTC 8a7d22d5-e9ba-45b8-b0dd-017cb62649f3 2012-05-24 06:48:16.752 UTC b594a08d-11fc-459b-9243-491bd5c0feda 2012-07-13 03:03:20.745 UTC 68edacf2-b990-4a31-b694-c8cacd99e465 2011-12-02 20:18:54.225 UTC 8a72c4e8-34e8-4850-99d8-7edfef99eb59 2012-07-10 16:28:46.151 UTC 5feed474-e086-436c-9dc8-547e6f6648bc 2012-05-25 14:20:34.984 UTC a8e9dc49-d486-4d55-a5a2-8de2e51149ea 2012-05-24 10:16:40.525 UTC b31c16f3-c7f3-4f45-8808-dbcca2286761 2012-05-28 13:50:16.908 UTC 8ed5c836-7421-4937-82a4-afd071d36068 2012-05-28 15:49:27.444 UTC 52aa7823-c531-4e64-9543-bbf57aa4c0de 2012-05-24 13:30:11.840 UTC 7e4d6ec1-007e-41b3-9b1a-39923c3843b6 2012-05-23 08:54:08.937 UTC 6ee5dac9-47db-4acf-8de3-4baf71ac2e0e 2012-05-24 07:12:27.913 UTC 225c56b9-df03-416e-bfef-ba2eb57a22cc 2012-05-24 11:45:35.231 UTC e9205450-f061-4220-a690-24780f575258 2012-05-24 10:09:38.171 UTC 16fc0fde-d715-4380-8c10-4f4362d71ac8 2012-05-24 14:14:29.971 UTC f0b2d523-78cc-49db-88a3-3c93c837b5fb 2012-05-29 09:17:34.988 UTC 8b1ca805-f1a3-45c0-8dd0-c2367fb62494 2012-05-29 09:24:10.559 UTC 7b6b6168-7421-4b1a-93e6-b6903bf56c49 2012-07-13 04:55:09.867 UTC 136247cc-6e2d-4a2c-a703-590419195f99 2012-05-29 07:49:50.399 UTC 9a5c4eb2-c8a0-4ab5-8733-2919f7a29c67 2011-12-04 20:23:12.582 UTC c23caeac-180a-417b-b101-afa124068d22 2012-05-24 11:18:13.132 UTC 5579e4f5-3b8a-41b5-a0b9-5a73d4d8f8b8 2012-05-28 15:22:26.463 UTC 65737da5-8b7f-4f23-88ab-d2da3ad8cd9e 2012-07-09 14:26:27.567 UTC b8ca8ea8-4261-47cf-826e-005f5d965883 2012-05-24 11:42:23.255 UTC 7c853e04-989f-467d-960a-8ad72355c5f2 2012-05-29 09:56:07.94 UTC ba6ce7ea-bec1-4cdc-8c9d-bae2d1086a9d 2012-05-24 10:04:37.281 UTC d53f5b51-874e-4b1e-809f-b66e9663cf8f 2012-05-28 15:41:56.31 UTC 365e4908-2036-409a-96c8-ce2adb53049d 2012-05-24 11:19:45.535 UTC 3e653fd3-19df-4ad7-b46b-a47192bf6639 2012-07-13 03:09:16.430 UTC c5bd0205-5369-43d1-99b8-97d96b84f515 2012-05-24 10:25:41.575 UTC e489f882-ec1f-492a-b233-89afc3a5d998 2012-05-29 08:19:59.344 UTC 4a0e6451-c4f7-4f7c-8865-ccecc158cde2 2012-07-16 14:22:28.219 UTC Purpose: The workflow maps a SNP (dbSNP id) to a gene (EntrezGene id). Author comments: The window for gene inclusion can be set using the set_width parameter. 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 13:09:21.798 UTC 4002f6bd-d804-4219-bf5d-1e3da51e388d 2012-07-14 02:58:10.79 UTC 0aaa6f86-7652-4191-91b9-933364dc640f 2012-05-28 13:39:00.742 UTC 9df76bf6-9c7e-47b3-bb5a-aadbcde0902c 2012-05-29 10:01:12.633 UTC 78bad41f-3d43-4052-9e7f-5619cb2866bc 2011-12-02 20:20:22.944 UTC 0f479371-ee41-44bb-b265-76c85e659653 2012-05-24 11:30:53.380 UTC e33d1b5a-4387-40af-8eb3-610183d068a1 2012-05-25 14:48:46.775 UTC 25b6de5f-396f-45c9-aaa2-e3277851f2c2 2011-12-05 09:29:51.46 UTC 6cba3d8f-b595-4757-8de7-d6c413032b29 2012-05-29 09:57:51.420 UTC f3fd6d4a-3b5a-4b82-a980-54ffd3b55e7b 2012-05-28 14:23:40.396 UTC 42a8db21-13e9-427a-9ed4-3ec73e5d09ad 2012-05-24 10:18:21.504 UTC 343ea31a-d25d-40e2-9d94-bb1063033339 2011-12-04 21:31:09.853 UTC 51b686d7-a903-449c-b10e-789e3eacaa77 2012-07-13 12:02:05.16 UTC 79dc3865-dde2-4c84-88e4-3069af419363 2012-07-13 20:26:29.179 UTC 880814c1-426f-4e59-8882-9241af442149 2012-05-28 15:50:25.224 UTC 689a09b4-747d-4616-8bea-f7d4c9cfad1d 2012-05-29 08:00:06.553 UTC c3eb4a90-1ef2-405e-8f56-e6f6ec2f87db 2012-05-28 15:46:04.713 UTC 86aae19c-517c-4f16-a964-4031ae65dcb2 2012-07-13 19:05:49.202 UTC 1b31e1dc-c604-41cd-ada0-7a630d9ab202 2012-05-23 09:50:23.48 UTC 396f1052-af35-4b0c-b81a-e6c80c9aa79b 2012-07-13 04:53:30.495 UTC c43d0c46-4007-4474-a96e-17f9e6f94623 2011-12-05 12:39:09.738 UTC 9754d989-1173-40df-bed9-a561f2c102c5 2012-07-13 11:32:04.849 UTC d5acc483-c168-468a-b09f-aa0e5bdd691e 2012-05-23 09:20:31.391 UTC 68b6a3a4-b582-4e29-9b7f-29c44c5c265b 2012-05-28 13:32:12.424 UTC 7dfa4a0e-911a-49e7-8fa9-867599fe1acb 2012-05-28 14:13:25.228 UTC c6954af8-29d3-49f2-9034-38847f1dd890 2012-05-28 14:28:31.311 UTC 9392534b-c27e-4185-9572-110f7d720aa3 2012-05-29 09:29:57.333 UTC 16ea68c5-c95d-4d0e-b08e-ea5c296e1ab3 2012-05-24 07:16:16.281 UTC d80fb6b7-8bf4-47e1-8f44-2a03441e8566 2012-05-23 09:22:12.952 UTC e8e28dad-160e-438f-b1a4-1bc0c952cee4 2012-05-29 08:10:33.77 UTC 2ff5f42c-ad5d-4855-afb6-994d95b56ad5 2011-12-05 12:45:17.858 UTC 8dc439f6-ae2e-4484-9f61-d5913cbbc83e 2012-05-24 11:21:29.155 UTC a4414467-dc1d-49ce-9f35-ee643b2b0a92 2012-05-24 07:40:13.121 UTC 58640859-5834-45bc-8133-a44a208b0b22 2012-07-09 14:41:53.348 UTC 162f2322-5cc8-4872-992d-154c488ae2be 2012-07-13 11:06:07.271 UTC 67bf7e76-47ea-4757-9d02-de763fba160b 2012-07-13 11:25:00.588 UTC 4ed47709-f143-454e-9df8-fc1ee053577c 2012-05-28 14:45:04.634 UTC 9e402cfc-fd28-4555-b7a0-75cb8851a823 2011-12-02 20:02:17.831 UTC 2e5e5024-9bf2-4adf-befb-f4585fe28e0e 2012-05-24 10:11:45.87 UTC 404b5061-dcee-4022-af0b-3f03ffb579d9 2012-07-10 13:47:51.897 UTC de94784e-ff3b-455a-b46d-115a3425f870 2012-07-12 22:58:00.866 UTC f961460c-2aac-418a-82c8-c6f9bb84bc25 2012-05-23 09:33:23.569 UTC f651a96e-f829-4d2c-812e-04b914799527 2012-05-24 14:16:55.168 UTC 8fba433b-1a50-4c58-9d88-4ce23c30b3ab 2011-12-04 20:34:38.768 UTC 82caace9-db1a-4b08-8528-7fed9f4fe3e3 2012-07-13 02:54:14.662 UTC 72797bde-afec-453a-831c-bc752526ec9b 2012-07-12 22:54:04.805 UTC 55699458-d13b-44c4-88a3-00b9a94d4bfd 2011-12-04 20:29:57.352 UTC 3b268f07-e232-491d-874d-fdcb50b1210f 2012-05-24 06:49:32.736 UTC aa106f23-15fa-4bde-8481-f38d9145ea4a 2012-05-28 15:24:47.801 UTC 418d93b2-546c-4e33-b77a-9ef284b18392 2011-12-05 09:21:49.671 UTC 6a975b77-984e-4396-92f0-74aaba68cc6e 2011-12-05 09:26:42.234 UTC 43260d53-f13f-4b02-8755-96eb198c7a13 2012-05-28 13:42:07.264 UTC 934a7783-3866-49c3-be45-9f6c00f25f04 2012-05-28 13:42:43.45 UTC d7b84de5-d36a-4090-8ab4-d37dde019b32 2012-05-28 14:18:44.466 UTC 56f48acf-de19-4709-991f-cdc768c578d8 2012-07-09 14:15:50.905 UTC 3d9a2e4e-9eaf-46ef-ac71-9ba04a52c4ba 2011-12-04 20:51:57.350 UTC 08489858-3622-42b4-8645-a7508a5a7eea 2012-05-24 11:49:05.799 UTC 12676d8e-8e07-44a8-adc3-246bed5f719e 2012-05-29 09:38:49.885 UTC f4bbc070-c3f5-48c7-bc3b-3e36572e755d 2012-05-28 15:21:02.683 UTC 56d2388f-4512-4039-8ac5-376509658156 2012-07-10 16:26:23.285 UTC e2e11b86-8b2e-4567-8da8-f508470a7206 2012-05-24 10:05:09.857 UTC 87ea0a35-0f9e-4fdb-bf4f-29dafeab759e 2011-12-05 09:20:36.359 UTC b6009e1a-5bd6-44e3-bdd6-9af7c90bdc52 2012-05-25 14:17:37.221 UTC 442fbd70-6edc-4aac-a52a-1e28af391883 2011-12-02 20:21:29.89 UTC cdf314f3-c07d-4299-9f12-b2fb34f16d71 2011-12-05 10:24:34.417 UTC f2dd9a4a-91c0-4c6a-aff4-43041ef6f4af 2012-05-24 10:07:59.36 UTC eedbb948-296f-448a-baec-81e9fe57a61f 2012-05-24 06:58:44.89 UTC eeaad7ea-4fbd-4283-b58f-68f1e9bb2a3c 2011-12-05 10:12:47.595 UTC ec2bec87-7bbf-4e50-a8c6-86a2aac5435f 2012-05-28 15:30:15.216 UTC c70559bc-32ea-45d5-9e0c-5c165efb1dce 2012-05-29 09:16:03.115 UTC 93602cc4-585d-434c-99f1-de25ffa08771 2012-07-12 23:08:39.267 UTC 44ce7b0d-aacc-4d8b-a074-befeb5e37ad5 2012-05-28 13:44:39.89 UTC e5e29e4d-d497-493a-9860-a8bd8d565754 2012-05-24 07:11:13.72 UTC SNP_ID2EntrezGene_ID 2012-07-16 14:26:57.243 UTC 92b50465-c47e-4f10-959f-6ac4ea412069 2012-07-13 10:53:40.120 UTC d2fab0b4-1886-49e3-b4e0-2ef4791554e3 2012-05-24 14:28:23.199 UTC 815b4de2-2533-4c65-acc1-61570ff0b7db 2012-05-28 14:46:29.632 UTC 8369db6a-1d67-44e8-bdc0-5586d6ac2665 2012-07-09 14:27:40.403 UTC fe69338b-803c-4d67-9aaa-b8710bd72317 2011-12-05 09:02:50.152 UTC bba91acb-8f29-45c8-b827-5fa8573f354d 2012-05-28 16:08:22.706 UTC e1852394-62d4-4ebf-b574-803b0a8e9276 2012-05-24 06:52:22.865 UTC Author: Harish Dharuri Contributor: Kristina Hettne 2012-07-18 13:06:17.451 UTC 5041e588-5b2c-46e2-bcd5-6df40c41b985 2012-07-13 10:56:58.41 UTC 32012e67-9983-4358-b01f-36b0cc8a7c73 2012-07-16 14:30:23.715 UTC 98a34165-cf45-4fbb-92dd-9714728b200e 2012-05-28 15:34:06.993 UTC bccb19ff-4ec7-48a0-ac70-c04c1b1c0ad1 2012-05-24 10:21:12.433 UTC 5267ab5b-b2c3-4b51-b145-616fca883313 2012-07-16 14:28:00.556 UTC 225e0718-30f5-4431-9c93-1367d0875f1c 2011-12-05 08:42:08.453 UTC 178f4858-1d1d-4749-993b-5c50c35fce9e 2012-05-29 09:34:11.328 UTC ba3d90fe-3286-4a20-9f70-1f96d3553cde 2012-05-25 14:43:53.153 UTC 18633aad-72f8-4de7-8355-7a3b41d2e782 2011-12-02 20:01:21.139 UTC 0dd472cc-fca4-40c7-befc-dc40d070613e 2012-05-28 12:57:45.369 UTC c79e9515-71ad-43a9-aaa5-b3c0b9f0c844 2012-05-23 09:32:11.351 UTC f894d03f-e142-475a-91e5-d97606dde276 2012-05-23 09:13:55.875 UTC 74431655-80e2-4cf3-b348-6b63f016e5f3 2012-07-13 19:10:56.745 UTC 4c18297b-d76f-494c-8e02-db4f29a0bb0d 2012-05-29 07:52:34.240 UTC 4f478714-44cb-4f1a-8f6f-93b7153386e5 2012-05-28 15:14:57.799 UTC e30dc445-e2a0-43f3-bfd7-083d248b55da 2012-05-28 13:40:30.818 UTC 21f88381-9624-4b53-b90d-338c89766640 2012-07-12 22:31:49.351 UTC b32a03e5-3a55-4c72-b3f5-5f041d859d25 2012-05-28 13:43:41.246 UTC 4df0a34f-79f5-4db9-8139-c816c4e8dca4 2011-12-05 08:57:23.769 UTC 2df74fd6-bad1-407a-96ed-5d789a5d790d 2012-07-12 22:38:14.266 UTC 6fafb7ef-e8da-4d79-a359-a589a488844a 2012-07-18 13:06:30.71 UTC 04371b1b-18bd-4405-a82d-c3db639977a0 2011-12-04 20:35:38.750 UTC d60af604-f923-4b3b-84a1-e5cab6eba64f 2012-05-24 10:23:12.911 UTC 9c66acfa-bc51-4c4a-aea4-52bbd719b3ee 2012-05-28 12:55:01.606 UTC 1a15a664-74ff-430c-8c5b-9a44b75c5d92 2012-05-24 10:24:32.110 UTC 8b743d45-0ed3-40af-b86c-621a622becd7 2012-05-25 15:13:17.443 UTC 50e39586-05d0-4cac-80e5-ca7476e4c62c 2012-05-28 13:06:09.328 UTC 1db5c6f1-a905-41a5-83c8-d8f79cd16ffd 2012-05-28 14:17:31.656 UTC 509480d2-5e56-46b9-a210-e1abd7f4fd59 2011-12-05 09:36:01.703 UTC 39ebc55b-a839-4ddb-854b-ff51dc377703 2012-05-28 14:11:19.840 UTC c0b817e8-664b-4f21-8737-6cdde6c33e72 2012-07-13 20:13:19.177 UTC bd0e27ad-006c-4572-bfba-39fb8ce0d5f7 2012-09-11 11:10:37.403 UTC 9dbddb98-bc13-49e4-99ea-abadf243ba48 2012-07-13 12:18:30.623 UTC 819a2da6-ac2f-450f-8898-ca47c9e17690 2012-05-28 13:26:14.402 UTC 354bd383-3970-46e5-a69d-756f249db3fd 2011-12-02 20:06:00.39 UTC 1f39dd51-fbda-49c3-b718-aeb0ff17961f 2012-05-24 14:39:02.624 UTC 3173b7fc-97e4-43c3-9494-e09ca7ab0009 2012-07-13 20:07:19.961 UTC 9fa557e0-a81d-4bb4-9f0f-1cbdfe7cc68e 2012-07-13 03:11:34.351 UTC 3b8a830b-befd-4274-a627-de73d272b6f8 2011-12-05 10:11:10.661 UTC 01b0a1c2-2ea1-42fb-8f77-3102cb2029c3 2012-05-24 08:02:12.628 UTC 388cc1a4-6e6d-4f55-b250-6783360f073d 2012-05-28 13:27:42.744 UTC 03b1577b-a1c9-4311-9e93-8297c6d54445 2012-07-16 14:23:43.831 UTC 09ff0ed8-017f-41e2-a5ac-8b25a86d1896 2012-05-24 07:14:01.348 UTC Match_concept_profilCutoff00 1 2013-02-05 19:53:47.84 UTC The number of resulting matched concepts that will be shown. 2012-04-16 12:36:29.53 UTC Match_concept_set00 The ConceptSet that is to be matched. A list of IDs for the predifined concept sets can be retrieved by running the List Concept Sets workflow (http://www.myexperiment.org/workflows/2999). The example ID corresponds to the concept set GO Biological Processes. 2013-02-05 20:18:48.820 UTC 5 2013-01-07 13:18:28.976 UTC Query_concept_ID00 The ConceptSet (a list of concept identifiers) to be queried. For example: 4275360 2012-04-16 12:39:57.499 UTC http://rdf.biosemantics.org/owl/concept#4275360 2013-02-05 20:12:35.528 UTC Match_concept_ID Concept ID of the matched concept. 2013-01-29 14:25:01.866 UTC <http://rdf.biosemantics.org/owl/concept#1156814/> 2013-01-29 14:24:54.220 UTC Similarity_score 0.0016150908923791584 2013-01-29 14:25:31.229 UTC List of similarity scores for the matched concept profiles. 2012-09-11 12:29:44.886 UTC getSimilarConceptProfilesPredefinedparameters0parameters00 The Web service takes a (list of) concept identifiers and the ID for the predefined concept set as input and calculates the matching score between the concept profiles of the concepts according to the scaled inner product. A list of IDs for the predifined concept sets can be retrieved by running the List Concept Sets workflow (http://www.myexperiment.org/workflows/2999). The example ID corresponds to the concept set GO Biological Processes. 2013-02-05 20:18:25.345 UTC net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivity http://ws.biosemantics.org/ConceptRecognizerService?wsdl getSimilarConceptProfilesPredefined net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetSimilarConceptProfilesPredefined_inputcutoffValue0conceptSetId0queryConceptProfileList0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity cutoffValue 0 'text/plain' false conceptSetId 0 'text/plain' false queryConceptProfileList 0 'text/plain' false output 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getSimilarConceptProfilesPredefined" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}getSimilarConceptProfilesPredefined"><s:elements><s:basetype optional="false" unbounded="false" typename="int" name="cutoffValue" qname="getSimilarConceptProfilesPredefined&gt;cutoffValue" /><s:basetype optional="false" unbounded="false" typename="int" name="conceptSetId" qname="getSimilarConceptProfilesPredefined&gt;conceptSetId" /><s:basetype optional="true" unbounded="false" typename="string" name="queryConceptProfileList" qname="getSimilarConceptProfilesPredefined&gt;queryConceptProfileList" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetSimilarConceptProfilesPredefined_outputinput0return00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false return 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getSimilarConceptProfilesPredefinedResponse" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}getSimilarConceptProfilesPredefinedResponse"><s:elements><s:complextype optional="true" unbounded="false" typename="matchingResult" name="return" qname="getSimilarConceptProfilesPredefinedResponse&gt;return"><s:elements><s:arraytype optional="true" unbounded="false" wrapped="true" typename="&gt;matchingResult&gt;MatchConceptProfileList" name="MatchConceptProfileList" qname="matchingResult&gt;MatchConceptProfileList"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="similarityScoreLists" name="SimilarityScoreLists" qname="matchingResult&gt;SimilarityScoreLists"><s:elementtype><s:complextype optional="false" unbounded="false" typename="scoreListImpl" name="" qname="{http://services.conceptrecognizer.lumc.nl/}scoreListImpl"><s:elements><s:arraytype optional="true" unbounded="true" wrapped="false" typename="stringDoubleTuple" name="QueryScoreTupleList" qname="scoreListImpl&gt;QueryScoreTupleList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="stringDoubleTuple" name="" qname="{http://services.conceptrecognizer.lumc.nl/}stringDoubleTuple"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="queryConceptID" qname="stringDoubleTuple&gt;queryConceptID" /><s:basetype optional="true" unbounded="false" typename="double" name="score" qname="stringDoubleTuple&gt;score" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:basetype optional="true" unbounded="false" typename="string" name="conceptId" qname="scoreListImpl&gt;conceptId" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="&gt;matchingResult&gt;SummedSimilarityScoreList" name="SummedSimilarityScoreList" qname="matchingResult&gt;SummedSimilarityScoreList"><s:elementtype><s:basetype optional="false" unbounded="false" typename="double" name="" qname="{http://www.w3.org/2001/XMLSchema}double" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetSimilarConceptProfilesPredefined_returninput0SummedSimilarityScoreList11MatchConceptProfileList11net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false MatchConceptProfileList 1 l('text/plain') 1 SimilarityScoreLists 0 'text/xml' 0 SummedSimilarityScoreList 1 l('text/plain') 1 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="true" unbounded="false" typename="matchingResult" name="return" qname="getSimilarConceptProfilesPredefinedResponse&gt;return"><s:elements><s:arraytype optional="true" unbounded="false" wrapped="true" typename="&gt;matchingResult&gt;MatchConceptProfileList" name="MatchConceptProfileList" qname="matchingResult&gt;MatchConceptProfileList"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="similarityScoreLists" name="SimilarityScoreLists" qname="matchingResult&gt;SimilarityScoreLists"><s:elementtype><s:complextype optional="false" unbounded="false" typename="scoreListImpl" name="" qname="{http://services.conceptrecognizer.lumc.nl/}scoreListImpl"><s:elements><s:arraytype optional="true" unbounded="true" wrapped="false" typename="stringDoubleTuple" name="QueryScoreTupleList" qname="scoreListImpl&gt;QueryScoreTupleList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="stringDoubleTuple" name="" qname="{http://services.conceptrecognizer.lumc.nl/}stringDoubleTuple"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="queryConceptID" qname="stringDoubleTuple&gt;queryConceptID" /><s:basetype optional="true" unbounded="false" typename="double" name="score" qname="stringDoubleTuple&gt;score" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:basetype optional="true" unbounded="false" typename="string" name="conceptId" qname="scoreListImpl&gt;conceptId" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="&gt;matchingResult&gt;SummedSimilarityScoreList" name="SummedSimilarityScoreList" qname="matchingResult&gt;SummedSimilarityScoreList"><s:elementtype><s:basetype optional="false" unbounded="false" typename="double" name="" qname="{http://www.w3.org/2001/XMLSchema}double" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetSimilarConceptProfilesPredefinedparametersgetSimilarConceptProfilesPredefined_inputoutputgetSimilarConceptProfilesPredefined_inputcutoffValueCutoffgetSimilarConceptProfilesPredefined_inputconceptSetIdMatch_concept_setgetSimilarConceptProfilesPredefined_inputqueryConceptProfileListQuery_concept_IDgetSimilarConceptProfilesPredefined_outputinputgetSimilarConceptProfilesPredefinedparametersgetSimilarConceptProfilesPredefined_returninputgetSimilarConceptProfilesPredefined_outputreturnMatch_concept_IDgetSimilarConceptProfilesPredefined_returnMatchConceptProfileListSimilarity_scoregetSimilarConceptProfilesPredefined_returnSummedSimilarityScoreList Authors: Kristina Hettne, Marco Roos Contributors: Reinout van Schouwen 2012-06-24 20:56:28.572 UTC 7986f41c-7556-45d9-bcb3-f557b69f3acc 2012-04-15 20:28:43.911 UTC 487ca7a4-63fa-45f9-baab-8f9a053ca9d0 2012-04-16 12:50:38.225 UTC da482794-4042-408d-adc4-c035dcb831ab 2012-04-16 12:41:12.260 UTC 8bdb17e0-10d5-42c5-9649-595b5b3ca226 2012-09-04 11:16:15.351 UTC 0d2ee2ad-e803-4529-afc2-e15bcd124a0c 2013-01-29 14:14:04.577 UTC 4d330136-ca78-4fa0-ad95-0d34b85f8a76 2011-09-20 15:56:44.26 UTC fafb8d94-026f-4044-b3ce-866fc199229b 2011-09-28 12:06:54.60 UTC e7d32565-d838-4bd0-987d-f03c4093d345 2013-01-29 14:21:26.174 UTC 9a1764af-8145-4c13-a849-38a031e6f2dd 2011-09-28 12:26:45.132 UTC abf2582f-e23f-40ff-b26a-c51da6f9e8f5 2013-02-05 11:11:56.753 UTC 4eb7b1fd-ec11-4fff-8a9b-ed9602b6bf8d 2013-02-05 20:16:31.628 UTC 46181b16-64e9-40aa-8dde-b32a9478fe1d 2011-09-27 15:29:17.819 UTC 98159653-b95c-4a97-b6b3-b400a68f0dc4 2013-01-29 14:17:24.662 UTC Match concept profiles with predefined set 2013-01-07 13:20:03.887 UTC ea38018e-ee90-4ccb-ab8e-78eeec907cad 2011-09-28 12:02:39.57 UTC 0dcad6f0-b77c-4d5d-ae1b-893a7b2436a6 2011-09-28 12:12:42.334 UTC 15145a87-30e2-4e04-97a9-10572ff64aae 2011-09-28 11:37:06.330 UTC e3d98432-1b19-474a-8c12-ed90f6aa23e8 2013-02-05 20:13:04.448 UTC abeb3495-f850-47e4-bc90-018b36584092 2011-09-28 12:24:29.380 UTC 55a9d4ab-19ee-4042-bf3d-5fabb52a3ab2 2012-06-24 20:56:30.877 UTC 0e2bcc6a-21cb-4a66-a50c-42fd8b2226aa 2013-01-07 13:15:58.306 UTC dacab209-3218-4181-a2f4-eaacfb1022b1 2013-02-04 10:17:42.374 UTC 1b7115f7-7832-4081-88df-c6ce4775238f 2011-09-28 11:35:31.328 UTC c55d2bf1-a3b9-46b1-a486-97b4b03eca20 2012-04-16 15:03:34.648 UTC 60d3ffca-7a97-485f-a391-6f8273236e1c 2013-02-01 11:26:19.951 UTC e48487a3-446f-42a1-9fcc-d820a9498ff0 2012-07-18 13:14:50.306 UTC 25ac05cb-87b1-4cee-926a-4fb5c6662b8f 2013-02-05 20:18:50.908 UTC dafd97bb-bd4c-4540-b335-d9cfe2d84108 2012-04-16 15:04:13.913 UTC 526ee9ee-6592-4472-90d4-f392659ea584 2013-01-29 12:44:50.692 UTC cc6b35c6-0d92-4ef7-ae5b-08eab3af670c 2013-01-07 13:21:45.613 UTC ae37940d-e39c-43c2-80bf-512e60710201 2012-04-16 12:45:48.511 UTC 477ba81b-f13d-41f2-ba19-e19f6104e36e 2012-09-11 12:14:41.164 UTC 19844d48-41a3-49e5-8cd3-5c3ccc40ec00 2013-01-07 13:19:35.160 UTC 494bf485-3d60-4900-88f6-060f54ef3969 2013-01-29 13:27:18.126 UTC de3149d9-6f9a-49cd-a542-91c18f65109d 2012-09-11 12:27:01.860 UTC 6036660d-2ac0-4369-a7f7-d208a0a26265 2012-09-11 12:31:12.75 UTC 9e39fe6a-c3da-4e04-a3ee-8c8dee6aa916 2013-01-28 15:31:38.841 UTC dacab209-3218-4181-a2f4-eaacfb1022b1 2013-02-05 11:18:43.126 UTC Purpose of workflow: The workflow can be used to match a set of concept profiles with another set of concept profiles. The result is a list of concepts ordered by their match to the query concept profiles. The workflow matches two sets of concept profiles. At the time of writing the concepts are derived from human, rat, and mouse terminologies, ontologies, and database identifiers. The profiles are lists of concepts ranked by their association with the identifying concept, as determined by co-location statistics computed from MedLine (up until 2009 at the time of writing). Author's comments: This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery. 2012-09-11 12:07:27.213 UTC 1d5bb33c-d18f-4d9c-9ead-487ab5271b7a 2011-09-27 15:37:33.997 UTC 680aa556-740a-433c-b63e-82a270a9d9e3 2013-01-29 15:48:25.704 UTC 233c6660-ebf6-47c8-af02-b1884424153d 2012-09-11 12:12:26.526 UTC 681cb800-d7cb-4786-8c64-585df6b607c7 2013-02-05 19:53:51.192 UTC a78cb530-6e91-48ac-8d8b-e6bc9ce7b0fa 2013-01-29 14:25:31.386 UTC 91ab33da-4da0-4e22-9542-7994c993b96a 2013-01-29 16:08:36.560 UTC ffd57175-7b65-4edb-9086-42bad4170b46 2011-09-27 13:41:33.82 UTC 09430282-326d-4c5b-85a8-28ddfc97753e 2011-09-27 15:31:47.87 UTC 3869f1dd-8db7-4881-b73a-4d55c99c6089 2013-02-01 15:53:09.746 UTC Filter_concepts_withConcept_ID00 The input concept ID (Erasmus MC ontology format). 2012-09-12 08:05:41.115 UTC http://rdf.biosemantics.org/owl/concept#3090691 2013-02-05 19:59:34.930 UTC Concepts_with_profiles Concept IDs (Erasmus MC ontology format) with profiles. 2012-09-12 08:06:21.459 UTC http://rdf.biosemantics.org/owl/concept#3090691 2013-02-05 19:59:27.917 UTC filterConceptsWithProfileparameters0parameters00 This Web service takes a (list of) concepts as input and returns the concept IDs of the concepts in the list that have a concept profile. 2012-09-12 08:04:13.528 UTC net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivity http://ws.biosemantics.org/ConceptRecognizerService?wsdl filterConceptsWithProfile net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokefilterConceptsWithProfile_outputinput0return00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false return 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="filterConceptsWithProfileResponse" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}filterConceptsWithProfileResponse"><s:elements><s:complextype optional="true" unbounded="false" typename="conceptSetWrapper" name="return" qname="filterConceptsWithProfileResponse&gt;return"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptIDsAsString" qname="conceptSetWrapper&gt;conceptIDsAsString" /></s:elements></s:complextype></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokefilterConceptsWithProfile_returninput0conceptIDsAsString00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false conceptIDsAsString 0 'text/plain' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="true" unbounded="false" typename="conceptSetWrapper" name="return" qname="filterConceptsWithProfileResponse&gt;return"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptIDsAsString" qname="conceptSetWrapper&gt;conceptIDsAsString" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokefilterConceptsWithProfile_inputconceptSet0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity conceptSet 0 'text/plain' false output 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="filterConceptsWithProfile" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}filterConceptsWithProfile"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptSet" qname="filterConceptsWithProfile&gt;conceptSet" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFilter_List_of_Strings_by_regexregex0stringlist1filteredlist11 This service filters the list at every occurrence of the specified regular expression. The regular expression provided in this case is an empty string: ^\S+$ 2013-02-05 19:40:01.968 UTC net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true regex 0 'text/plain' java.lang.String true filteredlist 1 l('text/plain') 1 workflow org.embl.ebi.escience.scuflworkers.java.FilterStringList net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregex_valuevalue00 The regular expression to be used for filtering. In this case: ^\S+$ 2013-02-05 19:40:36.304 UTC net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity ^\S+$ net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokefilterConceptsWithProfileparametersfilterConceptsWithProfile_inputoutputfilterConceptsWithProfile_outputinputfilterConceptsWithProfileparametersfilterConceptsWithProfile_returninputfilterConceptsWithProfile_outputreturnfilterConceptsWithProfile_inputconceptSetConcept_IDFilter_List_of_Strings_by_regexregexregex_valuevalueFilter_List_of_Strings_by_regexstringlistfilterConceptsWithProfile_returnconceptIDsAsStringConcepts_with_profilesFilter_List_of_Strings_by_regexfilteredlist f277c166-a637-46cb-8057-994bca43747c 2013-02-05 19:59:34.988 UTC 2c1a5ea4-a6b9-42e4-9058-89fa645166a5 2013-02-05 20:30:21.742 UTC 9534e0b4-b900-494d-8406-0962864ff722 2013-01-28 15:05:57.217 UTC d329fbae-c150-4b5b-87d5-9ca191669ec8 2013-02-05 19:40:36.400 UTC 23a69643-b9c9-4163-8a19-dfa1078b2713 2012-09-12 07:55:47.752 UTC Creator: Kristina Hettne on behalf of the BioSemantics group Contribution: Reinout van Schouwen (Web service) 2012-09-12 08:07:05.643 UTC 326ad476-7c6e-435b-8003-8ba9e7ad1b12 2012-09-12 08:07:46.534 UTC This workflow removes concepts that have no concept profile in the concept profile database, since only concepts with a concept profile can be used for concept profile matching. 2013-02-05 20:30:19.995 UTC 88f2a1fc-f70d-4c2a-965a-20fa0b0c4d84 2013-02-05 11:20:15.662 UTC Filter concepts with profiles 2012-09-12 08:07:23.356 UTC DatabaseID_to_ConceptIDDatabaseID00 EG 2012-04-24 23:16:44.86 UTC Identifier for databases, e.g. EG for Entrez Gene Possible values: EG, Entrez Gene 2012-06-25 20:38:10.999 UTC IDvalue00 3064 2012-04-24 23:17:45.507 UTC Identifier value, e.g. 3064 for HTT when DatabaseID=EG 2012-06-25 20:37:53.622 UTC Concept_IDs 3097212 2012-04-24 23:19:25.744 UTC Concept Identifiers for the given input, e.g. 3097212 for EG.3064 2012-04-24 23:19:16.717 UTC mapDatabaseIDToConceptIDsparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivity http://ws.biosemantics.org/ConceptRecognizerService?wsdl mapDatabaseIDToConceptIDs net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 3 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemapDatabaseIDToConceptIDs_inputID0database0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity database 0 'text/plain' false ID 0 'text/plain' false output 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="mapDatabaseIDToConceptIDs" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}mapDatabaseIDToConceptIDs"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="database" qname="mapDatabaseIDToConceptIDs&gt;database" /><s:basetype optional="true" unbounded="false" typename="string" name="ID" qname="mapDatabaseIDToConceptIDs&gt;ID" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemapDatabaseIDToConceptIDs_outputinput0return00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false return 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="mapDatabaseIDToConceptIDsResponse" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}mapDatabaseIDToConceptIDsResponse"><s:elements><s:complextype optional="true" unbounded="false" typename="conceptSetWrapper" name="return" qname="mapDatabaseIDToConceptIDsResponse&gt;return"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptIDsAsString" qname="conceptSetWrapper&gt;conceptIDsAsString" /></s:elements></s:complextype></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemapDatabaseIDToConceptIDs_returninput0conceptIDsAsString00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false conceptIDsAsString 0 'text/plain' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="true" unbounded="false" typename="conceptSetWrapper" name="return" qname="mapDatabaseIDToConceptIDsResponse&gt;return"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptIDsAsString" qname="conceptSetWrapper&gt;conceptIDsAsString" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemapDatabaseIDToConceptIDsparametersmapDatabaseIDToConceptIDs_inputoutputmapDatabaseIDToConceptIDs_inputIDIDvaluemapDatabaseIDToConceptIDs_inputdatabaseDatabaseIDmapDatabaseIDToConceptIDs_outputinputmapDatabaseIDToConceptIDsparametersmapDatabaseIDToConceptIDs_returninputmapDatabaseIDToConceptIDs_outputreturnConcept_IDsmapDatabaseIDToConceptIDs_returnconceptIDsAsString Authors: Marco Roos on behalf of the BioSemantics group Contributors: Web Service by Reinout van Schouwen Additional annotations by Kristina Hettne 2012-07-18 13:12:00.232 UTC c2cbb1b4-e2b2-4c45-9dfd-5323f702be83 2012-04-24 23:22:49.83 UTC d2f0a621-0e45-43b7-bd56-11c61a1c8df9 2012-07-18 13:13:11.179 UTC 7ecf19fa-7ed5-489c-82e5-9b2468795c30 2012-09-04 11:14:44.543 UTC c690ec55-e66d-4cde-a257-f219ab141679 2013-02-05 11:51:05.313 UTC 60ef0156-46c6-4368-a578-e6a26823caba 2013-01-28 15:03:01.417 UTC 80ee33e8-dddc-4d0f-aef9-ce9790e69904 2012-04-24 23:12:44.984 UTC 0b447fad-9299-453c-9195-e00c9fb687a7 2012-04-24 23:20:02.840 UTC Purpose: This workflow maps input Identifiers, common database identifiers, to the Concept Identifiers from the EMC ontology. Result: Concept Identifiers from the EMC ontology. Resources: Table of database identifiers and concept identifiers. Database identifiers from ... EMC ontology compiled from ... Comments: This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery. 2012-07-18 13:12:53.96 UTC cdf66f51-8d56-4a5f-87c7-5b8dbd434ee8 2012-07-11 14:23:57.252 UTC 14fee9a1-cd21-44f2-9f28-4f2362b8d667 2012-06-25 20:39:09.656 UTC DatabaseID_to_ConceptID 2012-04-24 23:22:45.412 UTC