GWAS_to_biomedical_cSNP_ID00rs26578792012-06-20 13:37:18.848 UTCID for the SNP (dbSNP format (http://www.ncbi.nlm.nih.gov/snp)).2012-06-20 15:17:25.383 UTCEntrezGene_database_type_ID00EG2012-06-20 14:32:52.489 UTCThe ID for the EntrezGene database (Erasmus MC ontology format).2012-06-25 12:35:49.147 UTCSet_width00The allows the user to set the flanking width for the gene for determining SNPs.2012-09-11 11:12:10.52 UTC1000002012-09-11 11:12:17.975 UTCMatch_concept_set0052013-02-05 12:13:59.34 UTCID of the predefined concept set to match with. These IDs can be retrieved by running the List Concept Sets workflow (http://www.myexperiment.org/workflows/2999). The example ID corresponds to the concept set GO Biological Processes.2013-02-05 12:13:53.474 UTCMatched_concepts_cutoff0012013-02-05 12:13:11.666 UTCMax number of concepts to return from the concept profile matching procedure.2013-02-05 12:13:08.874 UTCCo_occurring_documents_cutoff0012013-02-05 12:14:25.107 UTCMax number of co-occurring documents to return for a concept pair.2013-02-05 12:15:11.105 UTCExplained_concepts_cutoff00Max number of explanatory concepts to return for a concept profile match.2013-02-05 12:11:48.4 UTC12013-02-05 12:11:51.443 UTCSimilarity_scoreConcept match similarity score from the matching procedure.2013-02-05 12:19:18.72 UTC0.12723954517092986
0.12213216266242487
0.07526888282184858
0.06889675626758272014-07-14 14:15:53.621 UTCMatch_concept_IDIDs for the concepts from the concept profile match.2013-02-05 12:20:06.783 UTChttp://rdf.biosemantics.org/emco/v1.5/concepts/C2246672
http://rdf.biosemantics.org/emco/v1.5/concepts/C1817356
http://rdf.biosemantics.org/emco/v1.5/concepts/C1156814
http://rdf.biosemantics.org/emco/v1.5/concepts/C11552602014-07-14 14:15:38.165 UTCCo_occurring_document_titleThe document titles for which the query and the match concept co-occur. 2014-07-14 14:12:09.561 UTCMIP/Aquaporin 0 represents a direct transcriptional target of PITX3 in the developing lens.
Phosphate-activated glutaminase (GLS2), a p53-inducible regulator of glutamine metabolism and reactive oxygen species.
Glycosyl phosphatidylinositol-linked blood group antigens and paroxysmal nocturnal hemoglobinuria.2014-07-14 14:12:20.606 UTCCo_occurring_document_IDThe document IDs for which the query and the match concept co-occur. The example IDs refers to PubMed IDs.2014-07-14 14:11:59.142 UTC21698120
20351271
85420262014-07-14 14:11:43.63 UTCMatch_concept_nameregulation of s phase
lens development in camera-type eye
glutamine metabolic process
regulation of complement activation2014-07-14 14:15:21.613 UTCNames for the concepts from the concept profile match.2013-02-05 12:20:11.759 UTCQuery_concept_nameNames of the genes the SNPs were mapped to (only concepts with concept profiles are shown).2013-02-05 12:16:07.435 UTCTIMELESS1
MIP26
GLS2
RBMS22014-07-14 14:13:59.725 UTCExplanatory_concept_nameTIMELESS1
Lens, Crystalline
glutamine
CD552014-07-14 14:14:40.821 UTCThe concept names of the explanatory concepts.2013-02-05 12:17:14.521 UTCExplanatory_concept_contribution92.77331829071045
17.372439801692963
39.47658836841583
47.895020246505742014-07-14 14:15:01.421 UTCThe 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 UTCExplanatory_concept_IDThe concept IDs of the explanatory concepts.2013-02-05 19:32:47.1 UTChttp://rdf.biosemantics.org/emco/v1.5/concepts/C3067636
http://rdf.biosemantics.org/emco/v1.5/concepts/C23317
http://rdf.biosemantics.org/emco/v1.5/concepts/C4354094
http://rdf.biosemantics.org/emco/v1.5/concepts/C30558702014-07-14 14:14:20.885 UTCEntrez_gene_IDThe database ID2014-06-11 09:09:21.450 UTCEG2014-06-11 09:09:24.929 UTCQuery_concept_IDConcept IDs of the genes the SNPs were mapped to (only concepts with concept profiles are shown).2013-02-05 12:15:44.881 UTChttp://rdf.biosemantics.org/emco/v1.5/concepts/C3067636
http://rdf.biosemantics.org/emco/v1.5/concepts/C3067219
http://rdf.biosemantics.org/emco/v1.5/concepts/C3054172
http://rdf.biosemantics.org/emco/v1.5/concepts/C30563772014-07-14 14:13:20.477 UTCSNP_ID2EntrezGene_IDSNP_ID0set_width0EntrezGene_ID22Purpose of component in workflow:
This component maps a SNP ID to EntrezGene IDs.2012-06-25 20:24:42.884 UTCnet.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeEntrezGeneID_to_ConceptIDDatabaseID0IDvalue0Concept_IDs11Purpose 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 UTCnet.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFilter_genes_with_profilesConcept_ID0Concepts_with_profiles11Purpose 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 UTCnet.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeMatch_concept_profilesMatch_concept_set0Cutoff0Query_concept_ID0Similarity_score11Match_concept_ID11Purpose 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 UTCnet.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFind_co_occurring_documentsCutoff_value0ConceptID_11ConceptID_21Document_title33Document_ID33Purpose 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 UTCnet.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGet_match_concept_nameConcept_ID0Concept_name00Purpose of component in workflow:
To retrieve the name of the concept from the ontology.2013-02-05 18:56:56.393 UTCnet.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGet_concept_ID_and_nameConcept_ID0Concept_name00Concept_ID00Purpose of component in workflow:
To retrieve the name of the concept from the ontology.2013-02-05 18:56:44.407 UTCnet.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExplain_concept_scorescutoff0A_ConceptID0C_ConceptID0B_ConceptContribution11B_ConceptName11B_ConceptID11Purpose of component in workflow:
This component retieves the concepts contributing most to the match perfomed in the Match_concept_profiles component.2013-02-05 18:55:19.528 UTCnet.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_Concept_name_listinputlist2outputlist11This service flattens the inputlist by one level. It returns the result of the flattening.2013-02-05 19:36:18.256 UTCnet.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivityinputlist2l(l(''))[Btrueoutputlist1l('')1workfloworg.embl.ebi.escience.scuflworkers.java.FlattenListnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_match_concept_ID_listinputlist2outputlist11This service flattens the inputlist by one level. It returns the result of the flattening.2013-02-05 19:36:07.688 UTCnet.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivityinputlist2l(l(''))[Btrueoutputlist1l('')1workfloworg.embl.ebi.escience.scuflworkers.java.FlattenListnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_concept_ID_listinputlist2outputlist11This service flattens the inputlist by one level. It returns the result of the flattening.2013-02-05 19:36:13.112 UTCnet.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivityinputlist2l(l(''))[Btrueoutputlist1l('')1workfloworg.embl.ebi.escience.scuflworkers.java.FlattenListnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSNP_ID2EntrezGene_IDSNP_IDSNP_ID2EntrezGene_IDset_widthEntrezGeneID_to_ConceptIDDatabaseIDEntrezGeneID_to_ConceptIDIDvalueFilter_genes_with_profilesConcept_IDMatch_concept_profilesMatch_concept_setMatch_concept_profilesCutoffMatch_concept_profilesQuery_concept_IDFind_co_occurring_documentsCutoff_valueFind_co_occurring_documentsConceptID_1Find_co_occurring_documentsConceptID_2Get_match_concept_nameConcept_IDGet_concept_ID_and_nameConcept_IDExplain_concept_scorescutoffExplain_concept_scoresA_ConceptIDExplain_concept_scoresC_ConceptIDFlatten_Concept_name_listinputlistFlatten_match_concept_ID_listinputlistFlatten_concept_ID_listinputlistSimilarity_scoreMatch_concept_IDCo_occurring_document_titleCo_occurring_document_IDMatch_concept_nameQuery_concept_nameExplanatory_concept_nameExplanatory_concept_contributionExplanatory_concept_IDEntrez_gene_IDQuery_concept_ID9abaa51a-ea9b-480f-970a-812916f1c4a72013-02-04 14:49:09.919 UTC1bc8cbea-e850-4e43-917f-ad233066686b2012-09-11 12:39:42.431 UTC25736105-7e2a-4169-a17c-f6df342feb912013-02-05 18:58:33.132 UTCaac97bee-07b3-46ce-b8ae-f8b958e198572013-04-03 10:39:40.653 UTC84d272a3-ab36-4aa1-ba06-e5d4be6ddaae2012-06-20 13:42:04.903 UTCab0c102a-402a-4bdd-a7f4-b6824e3befb42013-04-05 12:24:06.19 UTC5ee6b306-17f4-4522-a9cf-a4f1fcc835782012-06-20 14:46:27.522 UTC48c1a107-fc59-43a2-b40b-3193dbee96212013-02-04 10:34:10.48 UTCfc5f9431-f6d8-4372-b2fc-df52b5b7517d2013-02-04 14:57:30.952 UTC8e7a0dad-8bcb-4808-a8ef-fc206aa673972012-07-11 14:25:39.502 UTC33f1f0d9-6566-44e8-8ddc-7791fe15aee22013-02-05 09:17:15.885 UTC50cd099f-d399-4e02-a4c8-870716274d922012-07-03 15:07:35.937 UTCed1e0f31-ddd6-4d2f-8ccd-7bb6700b3b452012-09-05 07:18:19.98 UTC689aca1a-e790-46da-89b4-8dd78a849d732013-02-01 15:53:13.435 UTCbaba66e2-155d-458c-86ce-c3d20f3bcdac2013-01-28 16:26:25.713 UTCf73d30e4-44c3-4265-921c-af28f7e121ef2012-09-11 15:01:15.447 UTCa1998c75-395a-43a8-bac1-41d27db568642013-02-05 16:34:19.12 UTCf08fe7b1-b124-4428-aa7f-aa4148445c242013-01-29 14:49:12.507 UTCf470d697-590a-4a5c-a5ac-0421a2a5779f2012-06-25 21:42:16.998 UTCb6e51879-3d2b-49d1-889b-ba650aa73b382012-09-05 08:53:51.612 UTCe25fa5e5-ff5a-4ad3-8fd0-980de6e994e22013-04-03 10:22:22.37 UTC65c0bb3a-4988-4234-bc43-f6a33084f7b42012-09-05 11:23:28.93 UTC349299f5-c1d4-41f9-a3c8-256fb4dedecb2012-06-20 14:50:32.447 UTC5c9f56ec-5fa4-46eb-9b49-05f99d24e3ee2012-09-11 15:21:33.102 UTCdc4bff60-a506-43bb-8573-3ef97c0316d22012-09-12 08:11:11.792 UTC8aba1fcc-9e6e-4b3a-94e2-15c3734571a72012-10-18 14:07:51.850 UTCffafa1a3-9198-4a07-81e5-f7443b9776c72012-07-11 15:15:22.568 UTC717e09ce-abfa-4f33-aa13-e916319a330a2012-09-12 07:06:36.668 UTCec1a8ee4-a30e-4050-a880-c4398dacfb3b2012-07-11 13:41:54.48 UTC38349196-b8df-45ba-be5b-8a1f1d62e1aa2013-02-04 14:53:22.525 UTCfeff77fe-9dd9-43cd-9f34-150ff8535ecc2013-01-29 14:44:48.318 UTC42dc2b06-15db-4e11-8b75-3a0e1aa66e892012-09-12 07:16:20.526 UTCe9a45dfa-bfae-4220-97bf-1c6d163a3e492012-06-25 21:25:02.684 UTC3edb70a4-e66f-4b96-8e12-3e440266e3752013-02-05 11:55:18.600 UTCf250679d-8be4-4282-bc0c-718b34b3cf902012-07-11 15:18:04.57 UTC9a17df2c-d08c-4ad8-b70d-17c26b2b2e672012-09-11 14:57:41.380 UTC8b9aed18-36d1-4f57-a885-b2a7c2bac8732012-07-04 08:59:08.521 UTCd415cfa3-3d04-4dd4-b1cb-b1c8658d5cc42012-06-25 10:06:26.773 UTC81c79d04-e062-47ba-a22b-ddec56289baa2013-01-29 16:09:05.655 UTCe90f9090-4f42-42c7-94a5-6296d92f7acb2012-06-25 12:08:23.148 UTC3422a432-9059-4f9b-a194-7e31a73e5b1e2012-09-12 13:39:27.31 UTCe45e1e2f-7573-4714-821f-314aa36f31d02012-07-04 12:01:02.382 UTCfce68cee-1931-4cd4-870b-3a1c0161ea312012-06-20 15:17:27.479 UTC4941fa84-f47f-4029-a615-27647edea50b2013-01-29 15:44:46.355 UTC31d2984c-7a07-4f6a-a9dc-ebb3772c17512012-09-07 15:00:44.730 UTC3a597170-9a73-40dc-822e-7411a48c84a02013-01-09 08:59:58.479 UTC6c275f7a-163e-41ce-913a-1074939d1b4b2013-02-05 12:21:26.778 UTC2a2de5a5-0450-49bf-b68e-c8910124c45a2012-06-20 13:19:11.570 UTCcf5196bc-9fc5-4116-ad0e-4e1ad8fcae1f2013-04-03 10:30:37.227 UTC644e2cd4-f219-4b7b-900a-a7b3f36bd9dd2012-07-18 13:29:04.78 UTC0d0232fd-9c2c-4f97-994b-a7b4fade3aeb2012-06-25 12:46:15.951 UTCfd21446e-6061-4805-b414-ac7cc30de5292013-02-01 11:26:28.673 UTC14dc58d3-a6ba-4c96-aa01-716dec0468962014-07-14 14:08:02.427 UTC4ab25513-b3b2-403e-8f4a-3ce8c4a56a532013-04-05 12:18:01.549 UTC10f45a70-24ed-46a0-94f5-27a8f45b195a2013-02-04 11:02:18.123 UTC92b312b4-d97a-4767-a54f-6d1e2ff411fb2013-01-28 15:17:26.598 UTC8a1c891f-626c-4eec-ad0a-2037af3518692012-06-25 12:40:54.246 UTCcaf05cc4-68f8-46f6-bdc6-3b140b2073462013-02-05 19:27:38.962 UTCAuthors:
Kristina Hettne
Contributors:
Reinout van Schouwen, Marco Roos, Harish Dharuri
2013-04-05 13:07:26.121 UTCbabf573f-83d7-4304-a59f-f1d53a19c4cc2012-09-11 10:06:58.293 UTC6f2a1eb8-b131-4182-852d-a7c38065b6f52013-02-05 16:28:25.603 UTC199ad955-4a64-4f3d-8afc-c4b1c2f9d08b2012-09-04 11:17:06.46 UTC3705a5da-0d54-42e7-8f69-5fcf173679c62013-02-05 19:23:31.320 UTC69d2b07d-1b28-4c30-ada7-202b4df5c8eb2012-07-11 14:56:13.37 UTCc44b9143-48dd-4172-b44d-6d39cb57b4212012-09-12 10:06:17.872 UTCGenome-Wide Association studies (GWAS) with metabolomic phenotypes yield several statistically significant SNP-metabolite associations. To understand the biological basis of the association, scientists typically dwell on identifying genes in the vicinity of the SNP and the possible pathways that the gene participates in. The information needed to arrive at an understanding of the mechanistic basis of the association requires integration of disparate data sources. The purpose of this workflow is to take the GWAS output consisting of SNP-metabolite associations and return genes present in the vicinity of the SNP ( for example, ± 100 kb of the snp), and the ranked biomedical concepts mined from the PubMed database relevant to these genes. The user is provided with the choice of setting the flanking width to interrogate around the SNP, the biomedical concept set to rank against the genes, the number of ranked concepts to return, the number of explaining concepts to return, the number of co-occurring documents to return, the type of gene database identifier, and the SNP identifier.
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.
2013-04-05 12:15:19.272 UTC35f8e419-c47b-4d49-8ba7-e7c0ef59955e2013-02-05 09:27:31.548 UTCf7d6584f-421e-41c6-b70c-bc019cf356722012-06-20 13:27:25.847 UTCf1fd209b-ec99-4713-b66b-b22e0d673f9f2012-09-04 11:18:48.47 UTC5a01765c-980c-4476-a60b-4eebb2a7d7e42013-02-05 09:05:11.428 UTCcab2e912-2388-43e9-9e31-f2e0743a31cc2013-02-05 10:56:52.361 UTCe6603d60-cfc2-4dc7-a8e4-3fbd83af38792012-06-25 12:15:42.217 UTC5075e001-4308-4145-b01b-163440ed659c2013-02-05 19:01:20.540 UTC0ae39656-960a-4b9c-a39e-c90370d970e42014-07-14 14:15:53.878 UTCe06f04ed-8f2b-43b6-b73c-0c1db8ecb2682012-06-25 11:42:30.855 UTC460d423f-3f88-4e17-b7dd-738b95cb117e2013-02-05 09:57:02.845 UTCab8c2488-f5c1-44c8-b5ec-719f624a8c412013-01-30 15:29:42.994 UTC2a6fb5b7-a2d0-4e3f-ab37-69e93c57a5d82013-02-04 14:50:05.607 UTC5552b01c-5913-4fc5-908f-64bcb8b9f94d2012-07-11 13:48:59.422 UTCf38cf673-7865-49c5-97b1-d60d7d2bc5cf2013-02-05 11:12:07.679 UTC4c055cd0-f134-4be3-a41a-11aad85725e12013-02-05 20:20:00.52 UTC02cbb28d-4940-47c4-a45d-8579a2f91d5d2013-01-29 15:50:22.589 UTC01bdae83-abec-4364-840c-27a1224cfbd92012-09-07 15:02:00.202 UTC1b7ef364-6500-4ee4-b82d-aa5d6081c42d2013-02-04 14:15:34.22 UTC438277ae-2f32-49b5-bfc1-9d92845351f22012-06-20 13:37:27.462 UTC41f7efc1-6d56-4034-9955-b23fd9d48ad92012-07-16 14:35:23.279 UTC1c82a7ea-5d2c-401b-b2e3-39a7c86a68ab2013-01-28 15:34:16.371 UTCd063979e-1984-4572-aa4b-ee0fa52394432012-07-18 13:25:29.879 UTC730ce424-62f4-4fc4-8392-f20d2be09da42012-09-12 10:44:52.756 UTCf53cdcc9-070e-4d5e-adf5-06b9bd9990f52012-07-18 13:29:42.117 UTC3814ffc0-f31a-4c96-820e-7cfba060cfd52012-06-25 12:17:59.1 UTCd8ede669-0d53-4bd1-9a37-ded1cdb5bb1c2012-06-25 12:03:27.734 UTC78a5bc98-afe7-49b5-a411-739894b618ca2012-06-25 11:56:37.177 UTC1e1fef40-ce71-4601-9138-53cf866679b22012-09-12 07:09:35.368 UTC081ca849-6a33-4ce7-807d-088976f280ff2012-09-12 12:36:07.673 UTC8db56f8b-2734-4bc1-a6a2-cc39b4f048192012-06-26 09:36:16.284 UTCb1e9fdfc-e7ec-4375-93dc-ecbc241a62572013-01-29 16:22:42.695 UTC21363a00-84f3-40e9-b676-4e5da44ee4b82013-01-29 15:46:43.251 UTC7471d9d8-88d1-4d96-9719-b347cd36c2ff2012-06-20 14:38:14.733 UTC616f2861-9708-4254-8ead-11fd31cdefe52013-02-05 11:35:58.360 UTCc7f596eb-b461-4a82-acde-e369c09d88062013-02-05 09:54:26.514 UTC42382374-0201-4786-a335-25db83eadff22012-06-20 14:54:43.422 UTC50e2a217-e1f1-4c16-ba48-38005280f9e92014-07-14 14:09:02.158 UTCaaa51b39-b160-4e85-a78c-cf6387ff30732012-07-11 12:59:11.88 UTCdd3d3cf8-5693-4031-94a2-688b70d8375f2012-06-24 20:57:10.828 UTC7c6624ce-6248-4a90-89a7-d55cde995e9f2013-02-05 09:43:39.757 UTCbc2328b4-2251-49e7-92a3-63c971b773c72012-07-11 12:57:09.537 UTCe6475d43-1bdc-4f31-a4b6-0d9642f617fa2013-02-05 09:07:27.795 UTC2dc8d590-d845-4bde-8cd1-369e4f1503a92012-06-20 13:35:14.359 UTCGWAS to biomedical concept2013-04-05 12:09:46.529 UTC92abab27-280e-457d-a60b-986ec4b53de32013-02-05 19:34:10.47 UTC42cc0e98-a177-4766-ade6-c4f6b634c96c2013-02-05 11:21:37.942 UTC5fb7380d-11e5-4b0a-baaa-c1f6a988070b2012-07-03 10:07:57.998 UTC38d29248-0454-4b55-baa3-d24fab456b1c2012-09-12 10:54:47.812 UTCabbd18c4-a83e-4ae4-93e9-4d577f05e9e52013-02-05 11:18:53.955 UTCa52ad8ed-0442-46dd-8a70-9d70108c856c2014-06-11 09:23:47.935 UTCb8f53807-cfa6-40d1-acfb-9aa59d38fa742012-06-23 14:14:48.33 UTC07e1051d-482b-431c-8bae-f8b65ec6a0a02012-06-25 12:47:08.190 UTCbada19cd-999b-4c78-996a-a8cf435bc1e82012-06-20 14:43:29.27 UTC5c98679f-949c-472a-8ab7-22c0013a10452012-06-20 12:55:14.538 UTC692af305-0370-4fde-86ff-b524d8a860a22013-04-05 12:38:00.276 UTC6fd3dd40-fd90-4a7e-908c-cd1bf85ca0fc2013-04-05 12:30:28.639 UTC9c29ff3b-6799-4086-b61b-3f5ddea195ad2013-02-05 12:24:00.388 UTC9cfa9e29-4cd6-4ea0-91ae-b50cbb6298db2012-09-11 13:02:19.614 UTC38e446d2-7e40-4b6b-a4c7-2597aab3cb1e2012-06-20 14:53:07.143 UTC31b663d8-6a90-4cb0-9c2a-4d0a1a33f4cc2013-03-28 11:15:02.476 UTCc9ce92ff-38c8-4b8b-84bb-df60c09e705d2012-09-11 15:29:14.683 UTCdd3da84c-4247-4a31-a533-cf055577d81b2013-02-05 11:42:37.21 UTC4eef1006-16ee-4410-8b29-1f39b0b30a142013-02-05 11:30:27.74 UTCf3137546-0733-49fb-bcad-fdf670a85c632013-02-05 19:37:51.70 UTC574cdcb3-529b-414c-8d27-c577a2a3e19c2013-02-04 14:43:47.363 UTCaa90d89d-a8e4-4d82-b828-c038cf9422d12012-06-25 18:08:31.488 UTCd207bb24-4f15-452e-82a4-addf9ed71b712012-07-03 10:30:04.342 UTCf95aab4d-710a-46ed-8d23-d248d5e4ac892012-06-25 11:38:25.616 UTC692af305-0370-4fde-86ff-b524d8a860a22013-04-05 12:49:11.888 UTC381a5e2b-e86e-4d6f-8458-eacc9250c96d2013-02-04 14:13:52.886 UTC321892b7-4e5c-4ce9-84b5-5944a1aa810e2013-04-05 13:07:30.768 UTCf3a6b09a-820e-4ab8-8eca-a496e38b8c142013-04-05 12:16:31.225 UTC724f40c1-2c66-4d0b-ab41-59eb2b0f83832012-06-24 20:54:25.360 UTCb43ac940-34c7-4327-9df8-dcc5e3587e552013-04-05 12:46:03.369 UTC31c7fb0f-67df-4ac2-8885-406acbcf6c452012-09-04 09:41:50.288 UTC63b150c1-06b2-4353-bf3c-a2fcf48d6f482012-09-07 15:04:00.35 UTCcb173e1d-c9f6-44fd-8e4a-feed0205ac272013-01-28 15:07:36.514 UTCfe747322-34f8-42fe-9aa8-aa202d6c6be92013-02-05 15:32:38.623 UTCe2ba0280-202b-4d6d-821b-b3539384e2372013-01-29 14:26:51.986 UTC6157699b-3fab-429a-a253-081473d7f7b92013-02-05 20:47:07.598 UTC78a68b62-d77c-4998-b032-041fda263d032012-09-12 12:59:34.796 UTC0d15cb49-d14e-425b-b2c1-d1a34ce4b6f92013-01-28 15:14:41.764 UTC31345088-55d0-4330-8a97-cff2d81405f52012-09-11 11:12:18.177 UTCa6d386e3-9404-4299-814d-07e20ced15d02012-09-11 12:54:25.760 UTCc84310b7-61d8-4111-a9d4-1cbbc70c27f52012-09-11 10:01:31.727 UTCGet_concept_informatConcept_ID00Concept ID of the concept to retrieve the name for.2013-02-05 20:06:06.218 UTChttp://rdf.biosemantics.org/emco/v1.5/concepts/C30541722014-07-14 14:05:19.719 UTCConcept_nameGLS22012-07-04 11:55:50.464 UTCThe name of the concept.2012-07-04 11:51:39.675 UTCConcept_IDhttp://rdf.biosemantics.org/emco/v1.5/concepts/C30541722014-07-14 14:05:45.704 UTCgetConceptProfileparameters0parameters00This Web service returns the concept profile for a given concept ID.2012-09-11 12:51:04.847 UTCnet.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://ws.biosemantics.org/ConceptProfileMiningService?wsdlgetConceptProfilenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetConceptProfile_inputconceptId0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivityconceptId0'text/plain'falseoutput0'text/xml'0<s:extensions 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>conceptId" /></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetConceptProfile_outputinput0return00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivityinput0'text/xml'java.lang.Stringfalsereturn0'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>return"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptId" qname="conceptProfileWrapper>conceptId" /><s:basetype optional="true" unbounded="false" typename="string" name="name" qname="conceptProfileWrapper>name" /><s:basetype optional="true" unbounded="false" typename="string" name="definition" qname="conceptProfileWrapper>definition" /><s:arraytype optional="true" unbounded="false" wrapped="true" typename=">conceptProfileWrapper>ConceptVector" name="ConceptVector" qname="conceptProfileWrapper>ConceptVector"><s:elementtype><s:complextype optional="false" unbounded="false" typename="stringDoubleTuple" name="" qname="{http://services.conceptrecognizer.lumc.nl/}stringDoubleTuple"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="queryConceptID" qname="stringDoubleTuple>queryConceptID" /><s:basetype optional="true" unbounded="false" typename="double" name="score" qname="stringDoubleTuple>score" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetConceptProfile_returninput0conceptId00name00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivityinput0'text/xml'java.lang.StringfalseconceptId0'text/plain'0name0'text/plain'0definition0'text/plain'0ConceptVector0'text/xml'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="true" unbounded="false" typename="conceptProfileWrapper" name="return" qname="getConceptProfileResponse>return"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptId" qname="conceptProfileWrapper>conceptId" /><s:basetype optional="true" unbounded="false" typename="string" name="name" qname="conceptProfileWrapper>name" /><s:basetype optional="true" unbounded="false" typename="string" name="definition" qname="conceptProfileWrapper>definition" /><s:arraytype optional="true" unbounded="false" wrapped="true" typename=">conceptProfileWrapper>ConceptVector" name="ConceptVector" qname="conceptProfileWrapper>ConceptVector"><s:elementtype><s:complextype optional="false" unbounded="false" typename="stringDoubleTuple" name="" qname="{http://services.conceptrecognizer.lumc.nl/}stringDoubleTuple"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="queryConceptID" qname="stringDoubleTuple>queryConceptID" /><s:basetype optional="true" unbounded="false" typename="double" name="score" qname="stringDoubleTuple>score" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetConceptProfileparametersgetConceptProfile_inputconceptIdgetConceptProfile_outputinputgetConceptProfile_returninputConcept_nameConcept_ID04d2b539-0ecf-47a2-b036-73e97581556f2012-07-04 11:56:13.312 UTC4b5150df-f12d-4f9a-a51e-a655e4c3cba12013-02-04 14:41:45.41 UTC80bc71ed-b511-4824-98e2-3e5add19aaae2012-09-07 14:29:24.729 UTCdea60608-70c7-4cf0-a8da-8513eb1a440a2012-09-04 11:17:36.783 UTCc6eaa639-5ee7-474e-9dbb-401927d650302012-09-11 12:49:35.323 UTC9f07ac09-c2b5-4d2a-bbcf-463c838632aa2014-07-14 14:06:03.367 UTC3afe257a-1246-4267-be82-ccb4203af53f2013-02-04 14:49:02.214 UTC2824bc65-af91-41c0-8912-e24151314a572012-09-11 12:51:06.419 UTCGet concept information2012-07-04 11:53:15.951 UTCcf644a3e-3942-4c42-b8c7-2f834fd110d42012-07-18 13:22:54.983 UTC0f9f0834-7609-4af4-b3dd-6a9452cda1232012-09-11 12:44:40.991 UTCThe workflow takes a concept ID as input and returns the ID, definition and name of the concept.
This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery.2012-07-18 13:22:23.330 UTCCreator:
Kristina Hettne on behalf of the BioSemantics group
Contributions:
Web services by Reinout van Schouwen2012-07-18 13:22:40.527 UTCb31a4602-eda2-485b-ad82-07db5fe820682012-07-04 11:54:39.48 UTCd9f930cb-1c79-46de-9935-e97cc62f5df72013-02-05 19:57:02.921 UTCa2ecda87-b5b6-473a-af29-b9fcf32ea7072012-09-11 12:40:55.902 UTCcefac9de-143f-47d7-b318-2af786d920462013-02-04 14:52:58.669 UTCff59aa50-8acd-40d6-b6dc-042b289db3142013-02-05 11:10:08.41 UTC83c3dad7-8d79-44e4-959a-e01ab677a6452013-02-05 20:06:08.228 UTCExplain_concept_scoresC_ConceptID00http://rdf.biosemantics.org/emco/v1.5/concepts/C11568142014-07-14 14:06:47.785 UTCThe concept id of the C concept.2012-09-11 09:01:25.824 UTCcutoff00Maximum number of explanatory concepts to return.2012-09-11 08:30:14.173 UTC12012-09-10 15:18:30.889 UTCA_ConceptID00http://rdf.biosemantics.org/emco/v1.5/concepts/C30541722014-07-14 14:07:01.343 UTCThe concept id of the A concept.2012-09-11 09:01:33.736 UTCB_ConceptNameThe concept name of the explanatory B concept.2012-09-11 09:01:44.136 UTCglutamine2014-06-11 09:20:05.533 UTCB_ConceptIDThe concept ID of the explanatory B concept.2012-09-11 09:01:40.385 UTChttp://rdf.biosemantics.org/emco/v1.5/concepts/C43540942014-07-14 14:07:36.928 UTCB_ConceptContributionThe contribution score, that is, the percentage of the contributions of the individual concepts to the coherence score (the average of the inner product scores of all possible concept pairs within the group).2012-09-11 08:58:01.819 UTC39.476588368415832014-06-11 09:19:30.525 UTCexplainScoresStringInputparameters0parameters00This Web service takes two concept ids as input and returns the top ranking "B" concepts according to Swanson's ABC model of discovery, where the relationships AB and BC are known and reported in the literature, and the implicit relationship AC is a putative new discovery. It might also be the case that AC is already known. In that case AC does not represent a new discovery but will still be returned by the Web service.
The concept contribution is also reported by the Web service. The concept contribution is the percentage of the contributions of the individual concepts to the coherence score (the average of the inner product scores of all possible concept pairs within the group).2012-09-11 08:57:10.939 UTCnet.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://ws.biosemantics.org/ConceptProfileMiningService?wsdlexplainScoresStringInputnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeexplainScoresStringInput_inputcutoffValue0conceptCUIsAsString0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivitycutoffValue0'text/plain'falseconceptCUIsAsString0'text/plain'falseoutput0'text/xml'0<s:extensions 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>cutoffValue" /><s:basetype optional="true" unbounded="false" typename="string" name="conceptCUIsAsString" qname="explainScoresStringInput>conceptCUIsAsString" /></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeexplainScoresStringInput_outputinput0return00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivityinput0'text/xml'java.lang.Stringfalsereturn0'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>return"><s:elements><s:arraytype optional="true" unbounded="false" wrapped="true" typename=">conceptContributionsWrapper>ConceptContributionTable" name="ConceptContributionTable" qname="conceptContributionsWrapper>ConceptContributionTable"><s:elementtype><s:complextype optional="false" unbounded="false" typename="conceptContribution" name="" qname="{http://services.conceptrecognizer.lumc.nl/}conceptContribution"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptName" qname="conceptContribution>conceptName" /><s:basetype optional="true" unbounded="false" typename="double" name="contribution" qname="conceptContribution>contribution" /><s:basetype optional="true" unbounded="false" typename="int" name="conceptId" qname="conceptContribution>conceptId" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeexplainScoresStringInput_returninput0ConceptContributionTable00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivityinput0'text/xml'java.lang.StringfalseConceptContributionTable0'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>return"><s:elements><s:arraytype optional="true" unbounded="false" wrapped="true" typename=">conceptContributionsWrapper>ConceptContributionTable" name="ConceptContributionTable" qname="conceptContributionsWrapper>ConceptContributionTable"><s:elementtype><s:complextype optional="false" unbounded="false" typename="conceptContribution" name="" qname="{http://services.conceptrecognizer.lumc.nl/}conceptContribution"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptName" qname="conceptContribution>conceptName" /><s:basetype optional="true" unbounded="false" typename="double" name="contribution" qname="conceptContribution>contribution" /><s:basetype optional="true" unbounded="false" typename="int" name="conceptId" qname="conceptContribution>conceptId" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokereturn_ConceptContributionTable_2input0ConceptContributionTable11net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivityinput0'text/xml'java.lang.StringfalseConceptContributionTable1l('text/xml')1<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:arraytype optional="true" unbounded="false" wrapped="true" typename=">conceptContributionsWrapper>ConceptContributionTable" name="ConceptContributionTable" qname="conceptContributionsWrapper>ConceptContributionTable"><s:elementtype><s:complextype optional="false" unbounded="false" typename="conceptContribution" name="" qname="{http://services.conceptrecognizer.lumc.nl/}conceptContribution"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptName" qname="conceptContribution>conceptName" /><s:basetype optional="true" unbounded="false" typename="double" name="contribution" qname="conceptContribution>contribution" /><s:basetype optional="true" unbounded="false" typename="int" name="conceptId" qname="conceptContribution>conceptId" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke2_ConceptContributionTableinput0contribution00conceptId00conceptName00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivityinput0'text/xml'java.lang.StringfalseconceptName0'text/plain'0contribution0'text/plain'0conceptId0'text/plain'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="conceptContribution" name="" qname="{http://services.conceptrecognizer.lumc.nl/}conceptContribution"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptName" qname="conceptContribution>conceptName" /><s:basetype optional="true" unbounded="false" typename="double" name="contribution" qname="conceptContribution>contribution" /><s:basetype optional="true" unbounded="false" typename="int" name="conceptId" qname="conceptContribution>conceptId" /></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemakeCommaSeparatedStringitem20item10output00This script concatenates the two input concept id strings and adds a comma in between.2012-09-11 08:29:47.911 UTCnet.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivityitem10text/plainjava.lang.Stringtrueitem20text/plainjava.lang.Stringtrueoutput00workflownet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeexplainScoresStringInputparametersexplainScoresStringInput_inputcutoffValueexplainScoresStringInput_inputconceptCUIsAsStringexplainScoresStringInput_outputinputexplainScoresStringInput_returninputreturn_ConceptContributionTable_2input2_ConceptContributionTableinputmakeCommaSeparatedStringitem2makeCommaSeparatedStringitem1B_ConceptNameB_ConceptIDB_ConceptContribution7d6ba6db-2552-4c15-b800-1789f5385d442012-09-07 15:18:14.352 UTCPurpose of workflow: This workflow takes two concept ids as input and returns the top ranking "B" concepts according to Swanson's ABC model of discovery, where the relationships AB and BC are known and reported in the literature, and the implicit relationship AC is a putative new discovery. It might also be the case that AC is already known. In that case AC does not represent a new discovery but will still be returned (see workflow example values). The B concepts are returned sorted on the percentage of the contributions of the individual concepts to the coherence score (the average of the inner product scores of all possible concept pairs within the group).
This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery.
2012-09-11 09:11:13.758 UTCfe118708-0284-4958-8a42-c9b099bc6a912014-06-11 09:20:11.67 UTCc416805f-aa9d-4d44-b434-f253935ed0ef2012-09-11 08:57:11.33 UTC09802e77-93ac-45ba-9ad5-e7bea33cda8b2013-02-05 20:09:38.174 UTC0faa8a91-3a1c-4e03-b74d-f271e7b962902012-04-16 12:55:56.499 UTCa6c096b8-050d-48bf-8b9c-114762aac26d2012-09-07 14:52:03.90 UTC8efd062c-22d8-4fc6-bfe4-ea8f96ba7e2a2012-04-16 12:58:21.8 UTCfc7ae322-fcac-41c5-b136-0767d52680b02012-03-21 13:53:26.66 UTC713fa342-cdf4-48b7-850d-abecb37b9b1f2012-09-11 08:58:13.328 UTCbb8d1d77-e3d2-4cee-aee9-3cd4e1bd85472012-01-06 12:38:00.681 UTC1ea652c5-572b-4b0a-b66d-5ae41a7b7fe12013-02-05 09:41:27.678 UTC89f2da6a-161b-47b1-a048-a65fd35f912c2012-01-06 11:47:16.46 UTC0e0f140b-920d-4b0b-a65b-c0537835a1c02014-07-14 14:07:51.606 UTCa260c127-7bbc-4dde-86a9-80647fcbb8622012-09-10 15:18:42.957 UTC8d4a9091-0ba9-468e-9883-7b08e5212cd22012-04-16 13:07:32.864 UTC7a995f89-0c37-48b9-b0f7-8eca5cd364202012-01-06 11:51:06.790 UTC4f826cfe-3950-4151-bbe6-bff67413be512012-09-07 15:22:15.103 UTC4b937a61-6180-48ce-a679-cf3ed1c8f2082012-09-11 08:58:54.136 UTC3c6eca00-e3a8-46b8-86bd-7c4b48a3ac772012-07-18 13:20:01.872 UTC6bab82da-54d0-4bc7-96fd-e5c5d3c6d77f2012-09-07 14:37:53.808 UTC2b762f5e-4473-4d48-b78f-df306600467a2012-09-11 09:11:13.838 UTC4bed166d-9815-4a35-a613-869b300b79732012-04-16 13:04:34.678 UTC8f284446-2578-4c4d-b81d-e842a463641b2012-09-07 15:34:00.455 UTC88e1d0d3-3377-4a21-a98f-19020444e6862012-09-07 14:58:20.922 UTCExplain concept scores2012-04-16 13:00:42.27 UTC90f0af1e-a653-4a85-889c-4120accdd9d92012-09-07 14:44:36.440 UTCCreator: Reinout van Schouwen on behalf of the BIoSemantics Group
Adaptations by Marco Roos and Kristina Hettne2012-09-11 09:02:52.112 UTC2b5167d3-3864-46c1-b761-b66ab721da542012-02-03 13:52:44.748 UTC9a6508bd-87c3-4d9c-99f2-9003b5b57df42012-09-11 09:01:50.31 UTC9e4c2fcc-6dcc-46d5-9edd-d7841389ef5c2012-04-17 08:22:27.551 UTC541a7a2d-e3e3-490d-885b-52d653a21d112012-02-03 11:42:15.89 UTC13050a9d-bdda-4de5-8bc7-8503457302cd2012-04-16 13:02:36.340 UTC142a2c6d-8e96-4c9f-ad64-da97fd4c25972012-09-04 11:16:44.759 UTCabaeb048-e186-4c8d-92d4-6b32b22603d82012-04-16 13:01:16.427 UTCSNP_ID2EntrezGene_IDSNP_ID00Use (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 UTCrs26578792012-07-16 14:27:52.745 UTCset_width001000002012-09-11 11:08:43.702 UTCThe allows the user to set the flanking width for the gene for determining SNPs.2012-09-11 11:08:34.646 UTCEntrezGene_ID8914
4284
283377
271652012-07-16 14:30:19.975 UTCA list of EntrezGene IDs.2012-07-16 14:29:53.708 UTCextract_snp_idstring0out100This extracts the contents (snp_ids) from the input.2012-09-11 10:15:10.813 UTCnet.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivitystring0text/plainjava.lang.Stringtrueout100workflownet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSplit_string_into_string_list_by_regular_expressionregex0string0split11This 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 UTCnet.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivitystring0'text/plain'java.lang.Stringtrueregex0'text/plain'java.lang.Stringtruesplit1l('text/plain')1workfloworg.embl.ebi.escience.scuflworkers.java.SplitByRegexnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregex_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity\nnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokehsapiens_snphsapiens_snp.snp_filter_filter0hsapiens_snp.chrom_start10hsapiens_snp.chr_name10This 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 UTCnet.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.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_Listinputlist2outputlist11This service flattens the inputlist by one level. It returns the result of the flattening.2012-09-11 11:07:13.494 UTCnet.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivityinputlist2l(l(''))[Btrueoutputlist1l('')1workfloworg.embl.ebi.escience.scuflworkers.java.FlattenListnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_List_2inputlist2outputlist11This service flattens the inputlist by one level. It returns the result of the flattening.2012-09-11 11:07:17.605 UTCnet.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivityinputlist2l(l(''))[Btrueoutputlist1l('')1workfloworg.embl.ebi.escience.scuflworkers.java.FlattenListnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeinput_chr_positionchr_in1in21in11chr_out11end_out11start_out11The 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 UTCnet.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivitychr_in1text/plainjava.lang.Stringtruein21text/plainjava.lang.Stringtruein11text/plainjava.lang.Stringtruechr_out11end_out11start_out11workflownet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokehsapiens_gene_ensemblhsapiens_gene_ensembl.chromosome_name_filter0hsapiens_gene_ensembl.end_filter0hsapiens_gene_ensembl.start_filter0hsapiens_gene_ensembl.entrezgene10This 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 UTCnet.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.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeextract_snp_idstringSplit_string_into_string_list_by_regular_expressionregexSplit_string_into_string_list_by_regular_expressionstringhsapiens_snphsapiens_snp.snp_filter_filterFlatten_ListinputlistFlatten_List_2inputlistinput_chr_positionchr_ininput_chr_positionin2input_chr_positionin1hsapiens_gene_ensemblhsapiens_gene_ensembl.chromosome_name_filterhsapiens_gene_ensemblhsapiens_gene_ensembl.end_filterhsapiens_gene_ensemblhsapiens_gene_ensembl.start_filterEntrezGene_ID131530e7-7bf2-440b-8ae4-7de74e4704262012-05-28 14:56:56.476 UTC8a7d22d5-e9ba-45b8-b0dd-017cb62649f32012-05-24 06:48:16.752 UTC122b2bb9-fdc0-4545-a673-487ec8eb4c9f2012-05-28 13:32:55.580 UTC0aaa6f86-7652-4191-91b9-933364dc640f2012-05-28 13:39:00.742 UTC470b1948-bcb8-401e-88ee-72172c9a1c752012-05-25 14:15:48.972 UTCbb845add-ef95-4621-ba20-7cdbcfd8895c2012-05-28 14:30:06.480 UTC663775b4-68ba-4dfe-8aa3-2a079a61805c2012-05-28 13:17:48.527 UTC489c0706-b993-44cc-878e-02cd52c0757a2012-05-28 13:28:40.258 UTC01b0a1c2-2ea1-42fb-8f77-3102cb2029c32012-05-24 08:02:12.628 UTCd5acc483-c168-468a-b09f-aa0e5bdd691e2012-05-23 09:20:31.391 UTC1f39dd51-fbda-49c3-b718-aeb0ff17961f2012-05-24 14:39:02.624 UTCd7cc4df4-9383-4543-870f-1beaa09c70f72012-05-29 10:05:40.594 UTC0550476f-da31-4066-b14f-f5f483f232fa2012-05-28 13:12:01.864 UTC8b743d45-0ed3-40af-b86c-621a622becd72012-05-25 15:13:17.443 UTCb594a08d-11fc-459b-9243-491bd5c0feda2012-07-13 03:03:20.745 UTCAuthor:
Harish Dharuri
Contributor:
Kristina Hettne2012-07-18 13:06:17.451 UTC9052cca1-3bac-456e-8964-bc5a97f24e122012-05-23 09:47:46.18 UTC3105f50e-deab-4464-8ac2-ab81746a8e1a2012-05-28 15:01:00.409 UTCf02a8cf2-7757-4252-b5ac-ad6729f9d80f2011-12-05 08:51:49.367 UTC74431655-80e2-4cf3-b348-6b63f016e5f32012-07-13 19:10:56.745 UTC0fe8a23c-ab84-4025-a5c0-27c652d9b7eb2012-05-28 15:06:02.685 UTC6ee5dac9-47db-4acf-8de3-4baf71ac2e0e2012-05-24 07:12:27.913 UTC354bd383-3970-46e5-a69d-756f249db3fd2011-12-02 20:06:00.39 UTC7c853e04-989f-467d-960a-8ad72355c5f22012-05-29 09:56:07.94 UTC773ad5ff-fa77-4807-9699-bc75f0be63b92011-12-04 19:55:52.32 UTC12676d8e-8e07-44a8-adc3-246bed5f719e2012-05-29 09:38:49.885 UTC178f4858-1d1d-4749-993b-5c50c35fce9e2012-05-29 09:34:11.328 UTC7dfa4a0e-911a-49e7-8fa9-867599fe1acb2012-05-28 14:13:25.228 UTCfe69338b-803c-4d67-9aaa-b8710bd723172011-12-05 09:02:50.152 UTCfcbc52b2-3f39-41cf-9eb2-f17badb0827c2012-05-29 09:25:28.151 UTCf651a96e-f829-4d2c-812e-04b9147995272012-05-24 14:16:55.168 UTCfe2b3810-d054-405f-8693-866dde2fcc602012-05-24 10:26:45.775 UTCd60af604-f923-4b3b-84a1-e5cab6eba64f2012-05-24 10:23:12.911 UTC799b2c7a-749d-4e85-96b8-57d4ce9d49a82012-05-28 13:49:09.988 UTC1f9fa403-1de0-4605-ae95-7964bb2b2a912012-05-23 09:00:46.292 UTCe70800df-db56-46cc-95c6-7331be9cfc222012-05-25 14:43:01.545 UTC55699458-d13b-44c4-88a3-00b9a94d4bfd2011-12-04 20:29:57.352 UTC880814c1-426f-4e59-8882-9241af4421492012-05-28 15:50:25.224 UTC42a8db21-13e9-427a-9ed4-3ec73e5d09ad2012-05-24 10:18:21.504 UTC9754d989-1173-40df-bed9-a561f2c102c52012-07-13 11:32:04.849 UTC79dc3865-dde2-4c84-88e4-3069af4193632012-07-13 20:26:29.179 UTC63150755-7e2c-46fa-9b18-d0af094e6bdb2012-07-13 11:16:52.800 UTCe33d1b5a-4387-40af-8eb3-610183d068a12012-05-25 14:48:46.775 UTC934a7783-3866-49c3-be45-9f6c00f25f042012-05-28 13:42:43.45 UTCde5376be-26df-4424-82f6-735797ecbb4d2011-12-04 19:54:39.289 UTC5579e4f5-3b8a-41b5-a0b9-5a73d4d8f8b82012-05-28 15:22:26.463 UTC92b50465-c47e-4f10-959f-6ac4ea4120692012-07-13 10:53:40.120 UTC56d2388f-4512-4039-8ac5-3765096581562012-07-10 16:26:23.285 UTC9392534b-c27e-4185-9572-110f7d720aa32012-05-29 09:29:57.333 UTC7984a5dc-f5ce-4991-aac7-0f4e761341972011-12-04 20:31:49.46 UTC8a72c4e8-34e8-4850-99d8-7edfef99eb592012-07-10 16:28:46.151 UTC1b31e1dc-c604-41cd-ada0-7a630d9ab2022012-05-23 09:50:23.48 UTC681bb15e-0cb0-4d46-b94d-50c8af23d5822011-12-05 10:05:00.123 UTC5041e588-5b2c-46e2-bcd5-6df40c41b9852012-07-13 10:56:58.41 UTC2ce8d6ce-78ef-4ba3-93f3-ae418cb04a042012-05-24 11:37:44.705 UTC1a15a664-74ff-430c-8c5b-9a44b75c5d922012-05-24 10:24:32.110 UTC9fa557e0-a81d-4bb4-9f0f-1cbdfe7cc68e2012-07-13 03:11:34.351 UTC16fc0fde-d715-4380-8c10-4f4362d71ac82012-05-24 14:14:29.971 UTC537f3d64-b1fd-43bd-9c13-ad4372dd7a512012-05-29 09:49:35.836 UTCeeaad7ea-4fbd-4283-b58f-68f1e9bb2a3c2011-12-05 10:12:47.595 UTCf4bbc070-c3f5-48c7-bc3b-3e36572e755d2012-05-28 15:21:02.683 UTCe5e29e4d-d497-493a-9860-a8bd8d5657542012-05-24 07:11:13.72 UTC4e8abbc2-c7d4-4763-a86a-b9238bc71a0a2012-05-23 09:46:24.941 UTCc14f091a-a1b6-43a6-af28-7599b1ddd8b12012-05-24 07:08:23.312 UTCf6370d45-5817-4828-98e5-8fa459e528762012-05-28 13:30:49.145 UTCf4ba5bba-e195-456c-9fce-4c7a04ef8e232012-05-28 13:11:04.53 UTC4ed47709-f143-454e-9df8-fc1ee053577c2012-05-28 14:45:04.634 UTC815b4de2-2533-4c65-acc1-61570ff0b7db2012-05-28 14:46:29.632 UTC3e653fd3-19df-4ad7-b46b-a47192bf66392012-07-13 03:09:16.430 UTCf961460c-2aac-418a-82c8-c6f9bb84bc252012-05-23 09:33:23.569 UTC86aae19c-517c-4f16-a964-4031ae65dcb22012-07-13 19:05:49.202 UTC396f1052-af35-4b0c-b81a-e6c80c9aa79b2012-07-13 04:53:30.495 UTCa8e9dc49-d486-4d55-a5a2-8de2e51149ea2012-05-24 10:16:40.525 UTC7732d491-9163-41d3-b43e-07f5e3710a5b2012-07-13 03:45:40.363 UTCPurpose:
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 UTC8ed5c836-7421-4937-82a4-afd071d360682012-05-28 15:49:27.444 UTCc0b817e8-664b-4f21-8737-6cdde6c33e722012-07-13 20:13:19.177 UTC1f56ace0-7a91-4cdb-80d2-078c96175c7a2012-05-24 07:59:59.475 UTCd9d5b914-c845-47f6-baa5-4965149a3eb62012-05-28 13:14:24.783 UTC98a34165-cf45-4fbb-92dd-9714728b200e2012-05-28 15:34:06.993 UTCd17e3593-215f-4c1d-8289-1111c40480362012-09-04 09:41:42.976 UTC3d9a2e4e-9eaf-46ef-ac71-9ba04a52c4ba2011-12-04 20:51:57.350 UTCf2dd9a4a-91c0-4c6a-aff4-43041ef6f4af2012-05-24 10:07:59.36 UTC9e402cfc-fd28-4555-b7a0-75cb8851a8232011-12-02 20:02:17.831 UTC3e9f3842-9dfc-4b71-a356-a1516667a0652012-05-28 16:29:16.964 UTC909dac87-86fa-4b27-b8f0-e58b6acf03292011-12-02 20:03:51.11 UTC323b72ad-2dad-491c-adcc-4b01f61d15c52012-07-13 03:48:12.471 UTC6a975b77-984e-4396-92f0-74aaba68cc6e2011-12-05 09:26:42.234 UTC4c18297b-d76f-494c-8e02-db4f29a0bb0d2012-05-29 07:52:34.240 UTC0dd472cc-fca4-40c7-befc-dc40d070613e2012-05-28 12:57:45.369 UTCc65a9a3a-909c-42a3-83cf-edd32d2e7aa92012-05-23 09:39:51.321 UTC4a0bd72f-205f-4fe2-aabf-4811716d04a32012-05-28 15:35:32.913 UTCde94784e-ff3b-455a-b46d-115a3425f8702012-07-12 22:58:00.866 UTCd7b84de5-d36a-4090-8ab4-d37dde019b322012-05-28 14:18:44.466 UTCSNP_ID2EntrezGene_ID2012-07-16 14:26:57.243 UTC225e0718-30f5-4431-9c93-1367d0875f1c2011-12-05 08:42:08.453 UTC720aa582-de73-463d-b2bc-ddd1699ebc4b2012-05-24 06:55:01.111 UTCc98b52f2-07a9-41c1-93e2-537baaca690f2012-05-25 14:45:00.606 UTCd2fab0b4-1886-49e3-b4e0-2ef4791554e32012-05-24 14:28:23.199 UTC8c5e8e26-1959-47e8-931a-f3d6053545242011-12-04 20:25:27.361 UTCf3fd6d4a-3b5a-4b82-a980-54ffd3b55e7b2012-05-28 14:23:40.396 UTCd80fb6b7-8bf4-47e1-8f44-2a03441e85662012-05-23 09:22:12.952 UTC33f3d4e3-80a9-44ec-8cfb-f84ebc21051c2012-05-28 12:44:30.573 UTCa4414467-dc1d-49ce-9f35-ee643b2b0a922012-05-24 07:40:13.121 UTC08489858-3622-42b4-8645-a7508a5a7eea2012-05-24 11:49:05.799 UTC3b8a830b-befd-4274-a627-de73d272b6f82011-12-05 10:11:10.661 UTC6fafb7ef-e8da-4d79-a359-a589a488844a2012-07-18 13:06:30.71 UTC52aa7823-c531-4e64-9543-bbf57aa4c0de2012-05-24 13:30:11.840 UTC8fba433b-1a50-4c58-9d88-4ce23c30b3ab2011-12-04 20:34:38.768 UTC4df0a34f-79f5-4db9-8139-c816c4e8dca42011-12-05 08:57:23.769 UTCe8e28dad-160e-438f-b1a4-1bc0c952cee42012-05-29 08:10:33.77 UTCb32a03e5-3a55-4c72-b3f5-5f041d859d252012-05-28 13:43:41.246 UTC56f48acf-de19-4709-991f-cdc768c578d82012-07-09 14:15:50.905 UTCf070ba04-399b-4422-94e9-7ac859c74e0a2012-05-28 14:48:31.535 UTC09ff0ed8-017f-41e2-a5ac-8b25a86d18962012-05-24 07:14:01.348 UTC8481be24-7358-4c81-a8fc-2b2b89f0069e2012-07-14 03:17:33.803 UTC2e5e5024-9bf2-4adf-befb-f4585fe28e0e2012-05-24 10:11:45.87 UTCb31c16f3-c7f3-4f45-8808-dbcca22867612012-05-28 13:50:16.908 UTC66d2a846-2d42-40a1-ac4a-0cb5ece59b2b2012-07-13 19:44:04.313 UTCaa106f23-15fa-4bde-8481-f38d9145ea4a2012-05-28 15:24:47.801 UTC819a2da6-ac2f-450f-8898-ca47c9e176902012-05-28 13:26:14.402 UTCd22656b0-2793-4ba7-8f90-1f80c27d54132012-07-10 12:46:34.516 UTCc5bd0205-5369-43d1-99b8-97d96b84f5152012-05-24 10:25:41.575 UTC4717b80f-c414-4cef-a833-5c74344454812011-12-04 20:17:49.522 UTCc79e9515-71ad-43a9-aaa5-b3c0b9f0c8442012-05-23 09:32:11.351 UTC6327f30f-f86f-407f-b65b-25dc8dd3a0222012-05-28 15:28:42.515 UTC780ac0b7-a424-49aa-9a7f-deb714fb52a62012-05-28 13:48:07.271 UTCd53f5b51-874e-4b1e-809f-b66e9663cf8f2012-05-28 15:41:56.31 UTC9916b6e6-526d-4583-b390-64518c4f06a12012-07-13 03:37:35.435 UTCc5edb75b-4a94-4aa8-80a7-05d5144327192011-12-05 12:41:04.327 UTC400ed11a-24fd-457a-a9b7-cc3ef85e8ad72012-05-24 11:44:12.16 UTC16c48a91-f694-48c0-9554-2e4694e04c612012-05-24 14:42:37.630 UTC661bc095-4dce-4ec9-885a-62cd4678a17d2012-05-25 15:39:45.220 UTC2082c444-8dc5-491d-98f0-a38e48f14ad22012-05-28 14:58:09.975 UTC59c48ad2-46fa-4c6a-920e-35585a726e7f2012-07-13 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UTC4f478714-44cb-4f1a-8f6f-93b7153386e52012-05-28 15:14:57.799 UTC0d757f59-9497-426a-b0dd-bdb68d3796d02012-05-24 11:52:38.509 UTCc3eb4a90-1ef2-405e-8f56-e6f6ec2f87db2012-05-28 15:46:04.713 UTC6dc63288-570b-4c6f-9d1b-3018852941bf2012-05-24 14:32:15.752 UTCe9205450-f061-4220-a690-24780f5752582012-05-24 10:09:38.171 UTC8dc439f6-ae2e-4484-9f61-d5913cbbc83e2012-05-24 11:21:29.155 UTC73ef94bb-6b99-402a-9305-e57e5ce4f5dc2012-07-13 10:41:55.216 UTC78bad41f-3d43-4052-9e7f-5619cb2866bc2011-12-02 20:20:22.944 UTC3b268f07-e232-491d-874d-fdcb50b1210f2012-05-24 06:49:32.736 UTC4002f6bd-d804-4219-bf5d-1e3da51e388d2012-07-14 02:58:10.79 UTC162f2322-5cc8-4872-992d-154c488ae2be2012-07-13 11:06:07.271 UTCb8ca8ea8-4261-47cf-826e-005f5d9658832012-05-24 11:42:23.255 UTCFind_co_occurring_doConceptID_111Concept ID for the input concept.2012-07-11 12:32:30.622 UTChttp://rdf.biosemantics.org/emco/v1.5/concepts/C11568142014-07-14 14:03:53.345 UTCConceptID_211Concept ID for the second concept.2012-07-11 12:33:12.79 UTChttp://rdf.biosemantics.org/emco/v1.5/concepts/C30541722014-07-14 14:02:45.346 UTCCutoff_value00The number of co-occurring documents to return.2012-07-11 12:30:11.639 UTC12012-07-11 12:30:25.642 UTCDocument_IDID of the returned document for which the two concepts co-occur.2013-02-05 19:51:31.314 UTC203512712014-07-14 14:04:30.737 UTCDocument_titlePhosphate-activated glutaminase (GLS2), a p53-inducible regulator of glutamine metabolism and reactive oxygen species.2014-07-14 14:04:09.40 UTCTitle of the returned document for which the two concepts co-occur.2013-02-05 19:51:24.400 UTCfindCoOccurringDocumentsparameters0parameters00This 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 UTCnet.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://ws.biosemantics.org/ConceptProfileMiningService?wsdlfindCoOccurringDocumentsnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050003net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokefindCoOccurringDocuments_inputconceptID10conceptID20cutoffValue0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivitycutoffValue0'text/plain'falseconceptID10'text/plain'falseconceptID20'text/plain'falseoutput0'text/xml'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="findCoOccurringDocuments" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}findCoOccurringDocuments"><s:elements><s:basetype optional="false" unbounded="false" typename="int" name="cutoffValue" qname="findCoOccurringDocuments>cutoffValue" /><s:basetype optional="true" unbounded="false" typename="string" name="conceptID1" qname="findCoOccurringDocuments>conceptID1" /><s:basetype optional="true" unbounded="false" typename="string" name="conceptID2" qname="findCoOccurringDocuments>conceptID2" /></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokefindCoOccurringDocuments_outputinput0return00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivityinput0'text/xml'java.lang.Stringfalsereturn0'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>return"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="cuiOwner" qname="supportingDocumentsWrapper>cuiOwner" /><s:basetype optional="true" unbounded="false" typename="string" name="cuiMember" qname="supportingDocumentsWrapper>cuiMember" /><s:basetype optional="true" unbounded="false" typename="int" name="originalSize" qname="supportingDocumentsWrapper>originalSize" /><s:arraytype optional="true" unbounded="false" wrapped="true" typename=">supportingDocumentsWrapper>SupportingDocumentsList" name="SupportingDocumentsList" qname="supportingDocumentsWrapper>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>title" /><s:basetype optional="false" unbounded="false" typename="int" name="PMID" qname="supportingDocument>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.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokefindCoOccurringDocuments_returninput0SupportingDocumentsList00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivityinput0'text/xml'java.lang.StringfalsecuiOwner0'text/plain'0cuiMember0'text/plain'0originalSize0'text/plain'0SupportingDocumentsList0'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>return"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="cuiOwner" qname="supportingDocumentsWrapper>cuiOwner" /><s:basetype optional="true" unbounded="false" typename="string" name="cuiMember" qname="supportingDocumentsWrapper>cuiMember" /><s:basetype optional="true" unbounded="false" typename="int" name="originalSize" qname="supportingDocumentsWrapper>originalSize" /><s:arraytype optional="true" unbounded="false" wrapped="true" typename=">supportingDocumentsWrapper>SupportingDocumentsList" name="SupportingDocumentsList" qname="supportingDocumentsWrapper>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>title" /><s:basetype optional="false" unbounded="false" typename="int" name="PMID" qname="supportingDocument>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.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokereturn_SupportingDocumentsListinput0SupportingDocumentsList11net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivityinput0'text/xml'java.lang.StringfalseSupportingDocumentsList1l('text/xml')1<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:arraytype optional="true" unbounded="false" wrapped="true" typename=">supportingDocumentsWrapper>SupportingDocumentsList" name="SupportingDocumentsList" qname="supportingDocumentsWrapper>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>title" /><s:basetype optional="false" unbounded="false" typename="int" name="PMID" qname="supportingDocument>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.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSupportingDocumentsList_SupportingDocumentsListinput0PMID00title00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivityinput0'text/xml'java.lang.Stringfalsetitle0'text/plain'0PMID0'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>title" /><s:basetype optional="false" unbounded="false" typename="int" name="PMID" qname="supportingDocument>PMID" /></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokefindCoOccurringDocumentsparametersfindCoOccurringDocuments_inputconceptID1findCoOccurringDocuments_inputconceptID2findCoOccurringDocuments_inputcutoffValuefindCoOccurringDocuments_outputinputfindCoOccurringDocuments_returninputreturn_SupportingDocumentsListinputSupportingDocumentsList_SupportingDocumentsListinputDocument_IDDocument_title739b02c1-fc07-41e3-b4e5-9a7174e4df7a2013-02-04 10:58:13.386 UTC9753fae4-dae9-40f6-a48b-94341d635fc02014-07-14 14:04:36.47 UTC58b2cab3-cf9d-419f-b41a-241990b5bc212013-02-05 19:51:48.145 UTCd42b0294-a5cf-4cfc-9635-26486e6139342012-09-04 11:17:59.103 UTCFind co-occurring documents2012-07-11 12:35:28.748 UTCPurpose:
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 UTC856c7313-b7d7-4522-a152-bf4f5bf5830d2013-02-04 14:13:02.886 UTC324bd118-08c0-4cc2-a3cf-86a0a6d802e02012-07-11 12:39:06.872 UTCCreator:
Kristina Hettne
Contributors:
Web services by Reinout van Schouwen
Additional annotations by Marco Roos2012-07-18 13:23:59.195 UTC6c42e1a2-7aec-4169-a712-79b6cf0729372012-07-11 12:36:19.218 UTC3beae759-c94b-45ff-99ab-d5471960ec112013-02-04 14:11:28.416 UTCe609f005-94e4-4f8c-b796-50f567459a972013-02-05 20:01:53.20 UTCa40a52c8-90c5-4755-a6c5-acae5f99b0e62012-09-11 12:53:08.81 UTCab19809c-64de-48aa-b573-563d94dd784c2012-07-11 12:34:09.767 UTC234b78c5-66c4-4e83-bbe0-a21ec539a50d2012-07-18 13:24:34.655 UTCDatabaseID_to_ConceptIDDatabaseID00EG2012-04-24 23:16:44.86 UTCIdentifier for databases, e.g. EG for Entrez Gene2014-06-11 09:23:12.407 UTCIDvalue0030642012-04-24 23:17:45.507 UTCIdentifier value, e.g. 3064 for HTT when DatabaseID=EG
2012-06-25 20:37:53.622 UTCConcept_IDsConcept Identifiers for the given input, e.g. 3058322 for EG.30642014-06-11 09:22:53.933 UTChttp://rdf.biosemantics.org/emco/v1.5/concepts/C30583222014-07-14 13:54:22.677 UTCmapDatabaseIDToConceptIDsparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://ws.biosemantics.org/ConceptProfileMiningService?wsdlmapDatabaseIDToConceptIDsnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050003net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemapDatabaseIDToConceptIDs_inputID0database0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivitydatabase0'text/plain'falseID0'text/plain'falseoutput0'text/xml'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="mapDatabaseIDToConceptIDs" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}mapDatabaseIDToConceptIDs"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="database" qname="mapDatabaseIDToConceptIDs>database" /><s:basetype optional="true" unbounded="false" typename="string" name="ID" qname="mapDatabaseIDToConceptIDs>ID" /></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemapDatabaseIDToConceptIDs_outputinput0return00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivityinput0'text/xml'java.lang.Stringfalsereturn0'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>return"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptIDsAsString" qname="conceptSetWrapper>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.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemapDatabaseIDToConceptIDs_returninput0conceptIDsAsString00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivityinput0'text/xml'java.lang.StringfalseconceptIDsAsString0'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>return"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptIDsAsString" qname="conceptSetWrapper>conceptIDsAsString" /></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregex_valuevalue00The regular expression to be used for filtering. In this case: ^\S+$2013-02-05 19:40:36.304 UTCnet.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity^\S+$net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFilter_List_of_Strings_by_regexregex0stringlist1filteredlist11This 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 UTCnet.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivitystringlist1l('text/plain')java.lang.Stringtrueregex0'text/plain'java.lang.Stringtruefilteredlist1l('text/plain')1workfloworg.embl.ebi.escience.scuflworkers.java.FilterStringListnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemapDatabaseIDToConceptIDsparametersmapDatabaseIDToConceptIDs_inputIDmapDatabaseIDToConceptIDs_inputdatabasemapDatabaseIDToConceptIDs_outputinputmapDatabaseIDToConceptIDs_returninputFilter_List_of_Strings_by_regexregexFilter_List_of_Strings_by_regexstringlistConcept_IDs80ee33e8-dddc-4d0f-aef9-ce9790e699042012-04-24 23:12:44.984 UTC14fee9a1-cd21-44f2-9f28-4f2362b8d6672012-06-25 20:39:09.656 UTCPurpose:
This workflow maps input Identifiers, common database identifiers, to the Concept Identifiers from the EMC ontology.
Result:
Concept Identifiers from the EMC ontology.
Resources:
Table of database identifiers and concept identifiers.
Database identifiers from ...
EMC ontology compiled from ...
Comments:
This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery.2012-07-18 13:12:53.96 UTCAuthors:
Marco Roos on behalf of the BioSemantics group
Contributors:
Web Service by Reinout van Schouwen
Additional annotations by Kristina Hettne2012-07-18 13:12:00.232 UTC451906fc-9e8d-482d-85cf-6ae9c5e334142014-06-11 09:22:54.18 UTC0b447fad-9299-453c-9195-e00c9fb687a72012-04-24 23:20:02.840 UTCd2f0a621-0e45-43b7-bd56-11c61a1c8df92012-07-18 13:13:11.179 UTCc2cbb1b4-e2b2-4c45-9dfd-5323f702be832012-04-24 23:22:49.83 UTC95bd024d-1eeb-442a-b08b-aab3b523d13c2014-06-11 09:23:14.290 UTC60ef0156-46c6-4368-a578-e6a26823caba2013-01-28 15:03:01.417 UTC21666c23-6313-43c7-8e28-a4f430bde3c42013-03-28 11:14:04.963 UTCDatabaseID_to_ConceptID2012-04-24 23:22:45.412 UTC20b51d5e-21f0-44aa-b0bf-1f0fec4d721d2014-07-14 13:54:27.763 UTC7ecf19fa-7ed5-489c-82e5-9b2468795c302012-09-04 11:14:44.543 UTCc690ec55-e66d-4cde-a257-f219ab1416792013-02-05 11:51:05.313 UTCcdf66f51-8d56-4a5f-87c7-5b8dbd434ee82012-07-11 14:23:57.252 UTCMatch_concept_profilCutoff0012013-02-05 19:53:47.84 UTCThe number of resulting matched concepts that will be shown. 2012-04-16 12:36:29.53 UTCMatch_concept_set00The ConceptSet that is to be matched. A list of IDs for the predifined concept sets can be retrieved by running the List Concept Sets workflow (http://www.myexperiment.org/workflows/2999). The example ID corresponds to the concept set GO Biological Processes.2013-02-05 20:18:48.820 UTC52013-01-07 13:18:28.976 UTCQuery_concept_ID00The query concepts (a comma-separated list of concept identifiers).2014-07-14 13:59:50.675 UTChttp://rdf.biosemantics.org/emco/v1.5/concepts/C3064256,http://rdf.biosemantics.org/emco/v1.5/concepts/C3061216,http://rdf.biosemantics.org/emco/v1.5/concepts/C3051663,http://rdf.biosemantics.org/emco/v1.5/concepts/C3059490,http://rdf.biosemantics.org/emco/v1.5/concepts/C3055883,http://rdf.biosemantics.org/emco/v1.5/concepts/C3067200,http://rdf.biosemantics.org/emco/v1.5/concepts/C3057680,http://rdf.biosemantics.org/emco/v1.5/concepts/C3065245,http://rdf.biosemantics.org/emco/v1.5/concepts/C3064136,http://rdf.biosemantics.org/emco/v1.5/concepts/C3057360,http://rdf.biosemantics.org/emco/v1.5/concepts/C3068478,http://rdf.biosemantics.org/emco/v1.5/concepts/C3051295,http://rdf.biosemantics.org/emco/v1.5/concepts/C3053273,http://rdf.biosemantics.org/emco/v1.5/concepts/C3051556,http://rdf.biosemantics.org/emco/v1.5/concepts/C3000408,http://rdf.biosemantics.org/emco/v1.5/concepts/C3054577,http://rdf.biosemantics.org/emco/v1.5/concepts/C3052008,http://rdf.biosemantics.org/emco/v1.5/concepts/C3047319,http://rdf.biosemantics.org/emco/v1.5/concepts/C3065318,http://rdf.biosemantics.org/emco/v1.5/concepts/C3057644,http://rdf.biosemantics.org/emco/v1.5/concepts/C3055667,http://rdf.biosemantics.org/emco/v1.5/concepts/C3064798,http://rdf.biosemantics.org/emco/v1.5/concepts/C3057037,http://rdf.biosemantics.org/emco/v1.5/concepts/C3052413,http://rdf.biosemantics.org/emco/v1.5/concepts/C3052193,http://rdf.biosemantics.org/emco/v1.5/concepts/C3066656,http://rdf.biosemantics.org/emco/v1.5/concepts/C3057861,http://rdf.biosemantics.org/emco/v1.5/concepts/C3056743,http://rdf.biosemantics.org/emco/v1.5/concepts/C3058841,http://rdf.biosemantics.org/emco/v1.5/concepts/C3000413,http://rdf.biosemantics.org/emco/v1.5/concepts/C3045026,http://rdf.biosemantics.org/emco/v1.5/concepts/C3000735,http://rdf.biosemantics.org/emco/v1.5/concepts/C3066648,http://rdf.biosemantics.org/emco/v1.5/concepts/C3058321,http://rdf.biosemantics.org/emco/v1.5/concepts/C3052192,http://rdf.biosemantics.org/emco/v1.5/concepts/C3062168,http://rdf.biosemantics.org/emco/v1.5/concepts/C3045451,http://rdf.biosemantics.org/emco/v1.5/concepts/C3064584,http://rdf.biosemantics.org/emco/v1.5/concepts/C3066277,http://rdf.biosemantics.org/emco/v1.5/concepts/C3057645,http://rdf.biosemantics.org/emco/v1.5/concepts/C3052203,http://rdf.biosemantics.org/emco/v1.5/concepts/C3055323,http://rdf.biosemantics.org/emco/v1.5/concepts/C30518572014-07-14 13:59:36.73 UTCMatch_concept_IDConcept ID of the matched concept.2013-01-29 14:25:01.866 UTChttp://rdf.biosemantics.org/emco/v1.5/concepts/C11599742014-07-14 14:01:23.203 UTCSimilarity_score0.4781231948867592014-07-14 14:01:39.642 UTCList of similarity scores for the matched concept profiles.2012-09-11 12:29:44.886 UTCgetSimilarConceptProfilesPredefinedparameters0parameters00The 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. 2014-07-14 14:01:48.707 UTCnet.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://ws.biosemantics.org/ConceptProfileMiningService?wsdlgetSimilarConceptProfilesPredefinednet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetSimilarConceptProfilesPredefined_inputcutoffValue0conceptSetId0queryConceptProfileList0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivitycutoffValue0'text/plain'falseconceptSetId0'text/plain'falsequeryConceptProfileList0'text/plain'falseoutput0'text/xml'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getSimilarConceptProfilesPredefined" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}getSimilarConceptProfilesPredefined"><s:elements><s:basetype optional="false" unbounded="false" typename="int" name="cutoffValue" qname="getSimilarConceptProfilesPredefined>cutoffValue" /><s:basetype optional="false" unbounded="false" typename="int" name="conceptSetId" qname="getSimilarConceptProfilesPredefined>conceptSetId" /><s:basetype optional="true" unbounded="false" typename="string" name="queryConceptProfileList" qname="getSimilarConceptProfilesPredefined>queryConceptProfileList" 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typename="getSimilarConceptProfilesPredefinedResponse" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}getSimilarConceptProfilesPredefinedResponse"><s:elements><s:complextype optional="true" unbounded="false" typename="matchingResult" name="return" qname="getSimilarConceptProfilesPredefinedResponse>return"><s:elements><s:arraytype optional="true" unbounded="false" wrapped="true" typename=">matchingResult>MatchConceptProfileList" name="MatchConceptProfileList" qname="matchingResult>MatchConceptProfileList"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="similarityScoreLists" name="SimilarityScoreLists" qname="matchingResult>SimilarityScoreLists"><s:elementtype><s:complextype optional="false" unbounded="false" typename="scoreListImpl" name="" qname="{http://services.conceptrecognizer.lumc.nl/}scoreListImpl"><s:elements><s:arraytype optional="true" unbounded="true" wrapped="false" typename="stringDoubleTuple" name="QueryScoreTupleList" qname="scoreListImpl>QueryScoreTupleList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="stringDoubleTuple" name="" qname="{http://services.conceptrecognizer.lumc.nl/}stringDoubleTuple"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="queryConceptID" qname="stringDoubleTuple>queryConceptID" /><s:basetype optional="true" unbounded="false" typename="double" name="score" qname="stringDoubleTuple>score" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:basetype optional="true" unbounded="false" typename="string" name="conceptId" qname="scoreListImpl>conceptId" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename=">matchingResult>SummedSimilarityScoreList" name="SummedSimilarityScoreList" qname="matchingResult>SummedSimilarityScoreList"><s:elementtype><s:basetype optional="false" unbounded="false" typename="double" name="" qname="{http://www.w3.org/2001/XMLSchema}double" 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xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="true" unbounded="false" typename="matchingResult" name="return" qname="getSimilarConceptProfilesPredefinedResponse>return"><s:elements><s:arraytype optional="true" unbounded="false" wrapped="true" typename=">matchingResult>MatchConceptProfileList" name="MatchConceptProfileList" qname="matchingResult>MatchConceptProfileList"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="similarityScoreLists" name="SimilarityScoreLists" qname="matchingResult>SimilarityScoreLists"><s:elementtype><s:complextype optional="false" unbounded="false" typename="scoreListImpl" name="" qname="{http://services.conceptrecognizer.lumc.nl/}scoreListImpl"><s:elements><s:arraytype optional="true" unbounded="true" wrapped="false" typename="stringDoubleTuple" name="QueryScoreTupleList" qname="scoreListImpl>QueryScoreTupleList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="stringDoubleTuple" name="" qname="{http://services.conceptrecognizer.lumc.nl/}stringDoubleTuple"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="queryConceptID" qname="stringDoubleTuple>queryConceptID" /><s:basetype optional="true" unbounded="false" typename="double" name="score" qname="stringDoubleTuple>score" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:basetype optional="true" unbounded="false" typename="string" name="conceptId" qname="scoreListImpl>conceptId" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename=">matchingResult>SummedSimilarityScoreList" name="SummedSimilarityScoreList" qname="matchingResult>SummedSimilarityScoreList"><s:elementtype><s:basetype optional="false" unbounded="false" typename="double" name="" qname="{http://www.w3.org/2001/XMLSchema}double" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetSimilarConceptProfilesPredefinedparametersgetSimilarConceptProfilesPredefined_inputcutoffValuegetSimilarConceptProfilesPredefined_inputconceptSetIdgetSimilarConceptProfilesPredefined_inputqueryConceptProfileListgetSimilarConceptProfilesPredefined_outputinputgetSimilarConceptProfilesPredefined_returninputMatch_concept_IDSimilarity_score9a1764af-8145-4c13-a849-38a031e6f2dd2011-09-28 12:26:45.132 UTCda482794-4042-408d-adc4-c035dcb831ab2012-04-16 12:41:12.260 UTCfafb8d94-026f-4044-b3ce-866fc199229b2011-09-28 12:06:54.60 UTC0d2ee2ad-e803-4529-afc2-e15bcd124a0c2013-01-29 14:14:04.577 UTC0dcad6f0-b77c-4d5d-ae1b-893a7b2436a62011-09-28 12:12:42.334 UTCe7d32565-d838-4bd0-987d-f03c4093d3452013-01-29 14:21:26.174 UTC15145a87-30e2-4e04-97a9-10572ff64aae2011-09-28 11:37:06.330 UTCedcb350f-992f-41cc-ada5-ff310b5ead042014-07-14 14:00:33.649 UTC4d330136-ca78-4fa0-ad95-0d34b85f8a762011-09-20 15:56:44.26 UTC487ca7a4-63fa-45f9-baab-8f9a053ca9d02012-04-16 12:50:38.225 UTCae37940d-e39c-43c2-80bf-512e607102012012-04-16 12:45:48.511 UTC1d5bb33c-d18f-4d9c-9ead-487ab5271b7a2011-09-27 15:37:33.997 UTCe3d98432-1b19-474a-8c12-ed90f6aa23e82013-02-05 20:13:04.448 UTCabeb3495-f850-47e4-bc90-018b365840922011-09-28 12:24:29.380 UTC55a9d4ab-19ee-4042-bf3d-5fabb52a3ab22012-06-24 20:56:30.877 UTCdacab209-3218-4181-a2f4-eaacfb1022b12013-02-04 10:17:42.374 UTCffd57175-7b65-4edb-9086-42bad4170b462011-09-27 13:41:33.82 UTC7986f41c-7556-45d9-bcb3-f557b69f3acc2012-04-15 20:28:43.911 UTC9e39fe6a-c3da-4e04-a3ee-8c8dee6aa9162013-01-28 15:31:38.841 UTCcc6b35c6-0d92-4ef7-ae5b-08eab3af670c2013-01-07 13:21:45.613 UTC25ac05cb-87b1-4cee-926a-4fb5c6662b8f2013-02-05 20:18:50.908 UTC1b7115f7-7832-4081-88df-c6ce4775238f2011-09-28 11:35:31.328 UTC3869f1dd-8db7-4881-b73a-4d55c99c60892013-02-01 15:53:09.746 UTC233c6660-ebf6-47c8-af02-b1884424153d2012-09-11 12:12:26.526 UTC98159653-b95c-4a97-b6b3-b400a68f0dc42013-01-29 14:17:24.662 UTC6036660d-2ac0-4369-a7f7-d208a0a262652012-09-11 12:31:12.75 UTCMatch concept profiles with predefined set2013-01-07 13:20:03.887 UTC665840dc-d949-4eda-95a2-c0d0963559682014-07-14 14:01:55.472 UTCe48487a3-446f-42a1-9fcc-d820a9498ff02012-07-18 13:14:50.306 UTC681cb800-d7cb-4786-8c64-585df6b607c72013-02-05 19:53:51.192 UTCAuthors:
Kristina Hettne, Marco Roos
Contributors:
Reinout van Schouwen2012-06-24 20:56:28.572 UTCea38018e-ee90-4ccb-ab8e-78eeec907cad2011-09-28 12:02:39.57 UTCa78cb530-6e91-48ac-8d8b-e6bc9ce7b0fa2013-01-29 14:25:31.386 UTC0e2bcc6a-21cb-4a66-a50c-42fd8b2226aa2013-01-07 13:15:58.306 UTC680aa556-740a-433c-b63e-82a270a9d9e32013-01-29 15:48:25.704 UTC60d3ffca-7a97-485f-a391-6f8273236e1c2013-02-01 11:26:19.951 UTCdafd97bb-bd4c-4540-b335-d9cfe2d841082012-04-16 15:04:13.913 UTC494bf485-3d60-4900-88f6-060f54ef39692013-01-29 13:27:18.126 UTC91ab33da-4da0-4e22-9542-7994c993b96a2013-01-29 16:08:36.560 UTC19844d48-41a3-49e5-8cd3-5c3ccc40ec002013-01-07 13:19:35.160 UTCdacab209-3218-4181-a2f4-eaacfb1022b12013-02-05 11:18:43.126 UTC09430282-326d-4c5b-85a8-28ddfc97753e2011-09-27 15:31:47.87 UTC8bdb17e0-10d5-42c5-9649-595b5b3ca2262012-09-04 11:16:15.351 UTCabf2582f-e23f-40ff-b26a-c51da6f9e8f52013-02-05 11:11:56.753 UTC477ba81b-f13d-41f2-ba19-e19f6104e36e2012-09-11 12:14:41.164 UTC4eb7b1fd-ec11-4fff-8a9b-ed9602b6bf8d2013-02-05 20:16:31.628 UTCc55d2bf1-a3b9-46b1-a486-97b4b03eca202012-04-16 15:03:34.648 UTC526ee9ee-6592-4472-90d4-f392659ea5842013-01-29 12:44:50.692 UTCPurpose of workflow: The workflow can be used to match a set of concept profiles with another set of concept profiles. The result is a list of concepts ordered by their match to the query concept profiles.
The workflow matches two sets of concept profiles. At the time of writing the concepts are derived from human, rat, and mouse terminologies, ontologies, and database identifiers. The profiles are lists of concepts ranked by their association with the identifying concept, as determined by co-location statistics computed from MedLine (up until 2009 at the time of writing).
Author's comments: This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery.
2012-09-11 12:07:27.213 UTCde3149d9-6f9a-49cd-a542-91c18f65109d2012-09-11 12:27:01.860 UTC46181b16-64e9-40aa-8dde-b32a9478fe1d2011-09-27 15:29:17.819 UTCGet_concept_informatConcept_ID00Concept ID of the concept to retrieve name and definition for.2012-07-04 11:50:31.405 UTChttp://rdf.biosemantics.org/emco/v1.5/concepts/C30541722014-07-14 14:08:39.638 UTCConcept_nameThe name of the concept.2012-07-04 11:51:39.675 UTCGLS22012-07-04 11:55:50.464 UTCgetConceptProfileparameters0parameters00This Web service returns the concept profile for a given concept ID.2012-09-11 12:51:04.847 UTCnet.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://ws.biosemantics.org/ConceptProfileMiningService?wsdlgetConceptProfilenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetConceptProfile_inputconceptId0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivityconceptId0'text/plain'falseoutput0'text/xml'0<s:extensions 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>conceptId" 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qname="{http://services.conceptrecognizer.lumc.nl/}getConceptProfileResponse"><s:elements><s:complextype optional="true" unbounded="false" typename="conceptProfileWrapper" name="return" qname="getConceptProfileResponse>return"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptId" qname="conceptProfileWrapper>conceptId" /><s:basetype optional="true" unbounded="false" typename="string" name="name" qname="conceptProfileWrapper>name" /><s:basetype optional="true" unbounded="false" typename="string" name="definition" qname="conceptProfileWrapper>definition" /><s:arraytype optional="true" unbounded="false" wrapped="true" typename=">conceptProfileWrapper>ConceptVector" name="ConceptVector" qname="conceptProfileWrapper>ConceptVector"><s:elementtype><s:complextype optional="false" unbounded="false" typename="stringDoubleTuple" name="" qname="{http://services.conceptrecognizer.lumc.nl/}stringDoubleTuple"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="queryConceptID" qname="stringDoubleTuple>queryConceptID" /><s:basetype optional="true" unbounded="false" typename="double" name="score" qname="stringDoubleTuple>score" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetConceptProfile_returninput0name00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivityinput0'text/xml'java.lang.StringfalseconceptId0'text/plain'0name0'text/plain'0definition0'text/plain'0ConceptVector0'text/xml'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="true" unbounded="false" typename="conceptProfileWrapper" name="return" qname="getConceptProfileResponse>return"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptId" qname="conceptProfileWrapper>conceptId" /><s:basetype optional="true" unbounded="false" typename="string" name="name" qname="conceptProfileWrapper>name" /><s:basetype optional="true" unbounded="false" typename="string" name="definition" qname="conceptProfileWrapper>definition" /><s:arraytype optional="true" unbounded="false" wrapped="true" typename=">conceptProfileWrapper>ConceptVector" name="ConceptVector" qname="conceptProfileWrapper>ConceptVector"><s:elementtype><s:complextype optional="false" unbounded="false" typename="stringDoubleTuple" name="" qname="{http://services.conceptrecognizer.lumc.nl/}stringDoubleTuple"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="queryConceptID" qname="stringDoubleTuple>queryConceptID" /><s:basetype optional="true" unbounded="false" typename="double" name="score" qname="stringDoubleTuple>score" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetConceptProfileparametersgetConceptProfile_inputconceptIdgetConceptProfile_outputinputgetConceptProfile_returninputConcept_nameCreator:
Kristina Hettne on behalf of the BioSemantics group
Contributions:
Web services by Reinout van Schouwen2012-07-18 13:22:40.527 UTCa2ecda87-b5b6-473a-af29-b9fcf32ea7072012-09-11 12:40:55.902 UTC4b5150df-f12d-4f9a-a51e-a655e4c3cba12013-02-04 14:41:45.41 UTCb31a4602-eda2-485b-ad82-07db5fe820682012-07-04 11:54:39.48 UTCdea60608-70c7-4cf0-a8da-8513eb1a440a2012-09-04 11:17:36.783 UTCd07c68fa-6eab-4eeb-b1bf-df3304fe9bb42014-07-14 14:08:55.29 UTC2824bc65-af91-41c0-8912-e24151314a572012-09-11 12:51:06.419 UTCThe workflow takes a concept ID as input and returns the ID, definition and name of the concept.
This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery.2012-07-18 13:22:23.330 UTCGet concept information2012-07-04 11:53:15.951 UTCc6eaa639-5ee7-474e-9dbb-401927d650302012-09-11 12:49:35.323 UTC0f9f0834-7609-4af4-b3dd-6a9452cda1232012-09-11 12:44:40.991 UTCcf644a3e-3942-4c42-b8c7-2f834fd110d42012-07-18 13:22:54.983 UTC80bc71ed-b511-4824-98e2-3e5add19aaae2012-09-07 14:29:24.729 UTC6a41503c-d915-4eac-998e-0d10ee8f32f12013-02-05 20:07:44.871 UTC04d2b539-0ecf-47a2-b036-73e97581556f2012-07-04 11:56:13.312 UTC3afe257a-1246-4267-be82-ccb4203af53f2013-02-04 14:49:02.214 UTCFilter_concepts_withConcept_ID00The input concept ID (Erasmus MC ontology format).2012-09-12 08:05:41.115 UTChttp://rdf.biosemantics.org/emco/v1.5/concepts/C3067636,http://rdf.biosemantics.org/emco/v1.5/concepts/C3067219,http://rdf.biosemantics.org/emco/v1.5/concepts/C3070198,http://rdf.biosemantics.org/emco/v1.5/concepts/C3054172,http://rdf.biosemantics.org/emco/v1.5/concepts/C30563772014-07-14 13:56:52.12 UTCConcepts_with_profilesConcept IDs (Erasmus MC ontology format) with profiles.2012-09-12 08:06:21.459 UTChttp://rdf.biosemantics.org/emco/v1.5/concepts/C3067636
http://rdf.biosemantics.org/emco/v1.5/concepts/C3067219
http://rdf.biosemantics.org/emco/v1.5/concepts/C3054172
http://rdf.biosemantics.org/emco/v1.5/concepts/C30563772014-07-14 13:55:50.125 UTCfilterConceptsWithProfileparameters0parameters00This 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 UTCnet.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://ws.biosemantics.org/ConceptProfileMiningService?wsdlfilterConceptsWithProfilenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokefilterConceptsWithProfile_outputinput0return00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivityinput0'text/xml'java.lang.Stringfalsereturn0'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>return"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptIDsAsString" qname="conceptSetWrapper>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.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokefilterConceptsWithProfile_returninput0conceptIDsAsString00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivityinput0'text/xml'java.lang.StringfalseconceptIDsAsString0'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>return"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptIDsAsString" qname="conceptSetWrapper>conceptIDsAsString" /></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokefilterConceptsWithProfile_inputconceptSet0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivityconceptSet0'text/plain'falseoutput0'text/xml'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="filterConceptsWithProfile" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}filterConceptsWithProfile"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptSet" qname="filterConceptsWithProfile>conceptSet" /></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFilter_List_of_Strings_by_regexregex0stringlist1filteredlist11This 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 UTCnet.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivitystringlist1l('text/plain')java.lang.Stringtrueregex0'text/plain'java.lang.Stringtruefilteredlist1l('text/plain')1workfloworg.embl.ebi.escience.scuflworkers.java.FilterStringListnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregex_valuevalue00The regular expression to be used for filtering. In this case: ^\S+$2013-02-05 19:40:36.304 UTCnet.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity^\S+$net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokefilterConceptsWithProfileparametersfilterConceptsWithProfile_outputinputfilterConceptsWithProfile_returninputfilterConceptsWithProfile_inputconceptSetFilter_List_of_Strings_by_regexregexFilter_List_of_Strings_by_regexstringlistConcepts_with_profilesCreator: Kristina Hettne on behalf of the BioSemantics group
Contribution: Reinout van Schouwen (Web service)2012-09-12 08:07:05.643 UTC23a69643-b9c9-4163-8a19-dfa1078b27132012-09-12 07:55:47.752 UTC88f2a1fc-f70d-4c2a-965a-20fa0b0c4d842013-02-05 11:20:15.662 UTCThis 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 UTC9534e0b4-b900-494d-8406-0962864ff7222013-01-28 15:05:57.217 UTCd329fbae-c150-4b5b-87d5-9ca191669ec82013-02-05 19:40:36.400 UTCf277c166-a637-46cb-8057-994bca43747c2013-02-05 19:59:34.988 UTC326ad476-7c6e-435b-8003-8ba9e7ad1b122012-09-12 08:07:46.534 UTCa3f0f779-0ce6-4b86-86de-b85e295d3ea92014-07-14 13:56:58.991 UTCFilter concepts with profiles2012-09-12 08:07:23.356 UTC2c1a5ea4-a6b9-42e4-9058-89fa645166a52013-02-05 20:30:21.742 UTC