SNPs_to_Concept_Set_SNP_ID00ID for the SNP (dbSNP format (http://www.ncbi.nlm.nih.gov/snp)).2012-06-20 15:17:25.383 UTCrs26578792012-06-20 13:37:18.848 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_set00ID 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 UTC52013-02-05 12:13:59.34 UTCMatched_concepts_cutoff00Max number of concepts to return from the concept profile matching procedure.2013-02-05 12:13:08.874 UTC12013-02-05 12:13:11.666 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_cutoff0012013-02-05 12:11:51.443 UTCMax number of explanatory concepts to return for a concept profile match.2013-02-05 12:11:48.4 UTCSimilarity_scoreConcept match similarity score from the matching procedure.2013-02-05 12:19:18.72 UTC2.689709811254242E-4
1.4602940663887876E-4
2.5138175063858174E-4
3.035844663481836E-42013-02-05 19:14:42.22 UTCMatch_concept_IDIDs for the concepts from the concept profile match.2013-02-05 12:20:06.783 UTC<http://rdf.biosemantics.org/owl/concept#1523019/>
<http://rdf.biosemantics.org/owl/concept#1159571/>
<http://rdf.biosemantics.org/owl/concept#1156814/>
<http://rdf.biosemantics.org/owl/concept#1155260/>2013-02-05 19:13:59.580 UTCCo_occurring_document_titleThe document IDs for which the query and the match concept co-occur. The example IDs refers to PubMed IDs.2013-02-05 12:20:50.566 UTC18029913
18787121
172373222013-02-05 12:21:57.447 UTCCo_occurring_document_IDEntrainment of the Drosophila circadian clock: more heat than light.
Dynamic control of slow water transport by aquaporin 0: implications for hydration and junction stability in the eye lens.
Energy metabolism in developing chicken lymphocytes is altered during the embryonic to posthatch transition.2013-02-05 12:21:40.55 UTCThe document titles for which the query and the match concept co-occur. 2013-02-05 12:21:05.975 UTCMatch_concept_nameNames for the concepts from the concept profile match.2013-02-05 12:20:11.759 UTCcircadian behavior
water transport
glutamine metabolic process
regulation of complement activation2013-02-05 12:22:45.270 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 UTCTIMELESS
MIP26
GLS2
RBMS22013-02-05 19:12:13.968 UTCExplanatory_concept_nameThe concept names of the explanatory concepts.2013-02-05 12:17:14.521 UTCtim
aquaporin activity
D-glutamine
CD552013-02-05 12:23:26.990 UTCExplanatory_concept_contributionThe 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 UTC30.8639258146286
44.40696835517883
42.68406629562378
48.198592662811282013-02-05 12:23:41.822 UTCExplanatory_concept_IDhttp://rdf.biosemantics.org/owl/concept#3055620
http://rdf.biosemantics.org/owl/concept#1753274
http://rdf.biosemantics.org/owl/concept#4275360
http://rdf.biosemantics.org/owl/concept#30950082013-02-05 19:33:08.193 UTCThe concept IDs of the explanatory concepts.2013-02-05 19:32:47.1 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/owl/concept#3108483
http://rdf.biosemantics.org/owl/concept#3088120
http://rdf.biosemantics.org/owl/concept#3092619
http://rdf.biosemantics.org/owl/concept#30881152013-02-05 19:10:23.169 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_IDs00Purpose 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_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.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.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_ID_listinputlistFlatten_Concept_name_listinputlistFlatten_match_concept_ID_listinputlistSimilarity_scoreMatch_concept_IDCo_occurring_document_titleCo_occurring_document_IDMatch_concept_nameQuery_concept_nameExplanatory_concept_nameExplanatory_concept_contributionExplanatory_concept_IDQuery_concept_ID574cdcb3-529b-414c-8d27-c577a2a3e19c2013-02-04 14:43:47.363 UTCa6d386e3-9404-4299-814d-07e20ced15d02012-09-11 12:54:25.760 UTC5c98679f-949c-472a-8ab7-22c0013a10452012-06-20 12:55:14.538 UTCd063979e-1984-4572-aa4b-ee0fa52394432012-07-18 13:25:29.879 UTC1b7ef364-6500-4ee4-b82d-aa5d6081c42d2013-02-04 14:15:34.22 UTC92abab27-280e-457d-a60b-986ec4b53de32013-02-05 19:34:10.47 UTCbaba66e2-155d-458c-86ce-c3d20f3bcdac2013-01-28 16:26:25.713 UTCcaf05cc4-68f8-46f6-bdc6-3b140b2073462013-02-05 19:27:38.962 UTC5c9f56ec-5fa4-46eb-9b49-05f99d24e3ee2012-09-11 15:21:33.102 UTCe9a45dfa-bfae-4220-97bf-1c6d163a3e492012-06-25 21:25:02.684 UTC50cd099f-d399-4e02-a4c8-870716274d922012-07-03 15:07:35.937 UTC8a1c891f-626c-4eec-ad0a-2037af3518692012-06-25 12:40:54.246 UTCfc5f9431-f6d8-4372-b2fc-df52b5b7517d2013-02-04 14:57:30.952 UTCa1998c75-395a-43a8-bac1-41d27db568642013-02-05 16:34:19.12 UTC31345088-55d0-4330-8a97-cff2d81405f52012-09-11 11:12:18.177 UTC78a68b62-d77c-4998-b032-041fda263d032012-09-12 12:59:34.796 UTC381a5e2b-e86e-4d6f-8458-eacc9250c96d2013-02-04 14:13:52.886 UTC4eef1006-16ee-4410-8b29-1f39b0b30a142013-02-05 11:30:27.74 UTC9c29ff3b-6799-4086-b61b-3f5ddea195ad2013-02-05 12:24:00.388 UTCffafa1a3-9198-4a07-81e5-f7443b9776c72012-07-11 15:15:22.568 UTC42382374-0201-4786-a335-25db83eadff22012-06-20 14:54:43.422 UTC7c6624ce-6248-4a90-89a7-d55cde995e9f2013-02-05 09:43:39.757 UTC35f8e419-c47b-4d49-8ba7-e7c0ef59955e2013-02-05 09:27:31.548 UTC38e446d2-7e40-4b6b-a4c7-2597aab3cb1e2012-06-20 14:53:07.143 UTCSNPs to Concept Set through Concept Profile Matching v22013-01-09 08:56:40.72 UTC31c7fb0f-67df-4ac2-8885-406acbcf6c452012-09-04 09:41:50.288 UTCec1a8ee4-a30e-4050-a880-c4398dacfb3b2012-07-11 13:41:54.48 UTCcab2e912-2388-43e9-9e31-f2e0743a31cc2013-02-05 10:56:52.361 UTCe45e1e2f-7573-4714-821f-314aa36f31d02012-07-04 12:01:02.382 UTC41f7efc1-6d56-4034-9955-b23fd9d48ad92012-07-16 14:35:23.279 UTCf38cf673-7865-49c5-97b1-d60d7d2bc5cf2013-02-05 11:12:07.679 UTC4941fa84-f47f-4029-a615-27647edea50b2013-01-29 15:44:46.355 UTCb1e9fdfc-e7ec-4375-93dc-ecbc241a62572013-01-29 16:22:42.695 UTCed1e0f31-ddd6-4d2f-8ccd-7bb6700b3b452012-09-05 07:18:19.98 UTCfce68cee-1931-4cd4-870b-3a1c0161ea312012-06-20 15:17:27.479 UTC3814ffc0-f31a-4c96-820e-7cfba060cfd52012-06-25 12:17:59.1 UTC69d2b07d-1b28-4c30-ada7-202b4df5c8eb2012-07-11 14:56:13.37 UTCabbd18c4-a83e-4ae4-93e9-4d577f05e9e52013-02-05 11:18:53.955 UTCf08fe7b1-b124-4428-aa7f-aa4148445c242013-01-29 14:49:12.507 UTCfd21446e-6061-4805-b414-ac7cc30de5292013-02-01 11:26:28.673 UTC2dc8d590-d845-4bde-8cd1-369e4f1503a92012-06-20 13:35:14.359 UTCf3137546-0733-49fb-bcad-fdf670a85c632013-02-05 19:37:51.70 UTC1bc8cbea-e850-4e43-917f-ad233066686b2012-09-11 12:39:42.431 UTC65c0bb3a-4988-4234-bc43-f6a33084f7b42012-09-05 11:23:28.93 UTC5075e001-4308-4145-b01b-163440ed659c2013-02-05 19:01:20.540 UTC2a6fb5b7-a2d0-4e3f-ab37-69e93c57a5d82013-02-04 14:50:05.607 UTC9cfa9e29-4cd6-4ea0-91ae-b50cbb6298db2012-09-11 13:02:19.614 UTCd207bb24-4f15-452e-82a4-addf9ed71b712012-07-03 10:30:04.342 UTCf95aab4d-710a-46ed-8d23-d248d5e4ac892012-06-25 11:38:25.616 UTC8aba1fcc-9e6e-4b3a-94e2-15c3734571a72012-10-18 14:07:51.850 UTC717e09ce-abfa-4f33-aa13-e916319a330a2012-09-12 07:06:36.668 UTC10f45a70-24ed-46a0-94f5-27a8f45b195a2013-02-04 11:02:18.123 UTCf53cdcc9-070e-4d5e-adf5-06b9bd9990f52012-07-18 13:29:42.117 UTC8e7a0dad-8bcb-4808-a8ef-fc206aa673972012-07-11 14:25:39.502 UTC8db56f8b-2734-4bc1-a6a2-cc39b4f048192012-06-26 09:36:16.284 UTC3705a5da-0d54-42e7-8f69-5fcf173679c62013-02-05 19:23:31.320 UTC689aca1a-e790-46da-89b4-8dd78a849d732013-02-01 15:53:13.435 UTCcb173e1d-c9f6-44fd-8e4a-feed0205ac272013-01-28 15:07:36.514 UTCfeff77fe-9dd9-43cd-9f34-150ff8535ecc2013-01-29 14:44:48.318 UTCf250679d-8be4-4282-bc0c-718b34b3cf902012-07-11 15:18:04.57 UTCb6e51879-3d2b-49d1-889b-ba650aa73b382012-09-05 08:53:51.612 UTC730ce424-62f4-4fc4-8392-f20d2be09da42012-09-12 10:44:52.756 UTC31d2984c-7a07-4f6a-a9dc-ebb3772c17512012-09-07 15:00:44.730 UTC38349196-b8df-45ba-be5b-8a1f1d62e1aa2013-02-04 14:53:22.525 UTCdd3da84c-4247-4a31-a533-cf055577d81b2013-02-05 11:42:37.21 UTC63b150c1-06b2-4353-bf3c-a2fcf48d6f482012-09-07 15:04:00.35 UTCAuthors:
Kristina Hettne, Marco Roos
Contributors:
Reinout van Schouwen, Marco Roos
2012-06-24 20:50:02.542 UTC3422a432-9059-4f9b-a194-7e31a73e5b1e2012-09-12 13:39:27.31 UTC1e1fef40-ce71-4601-9138-53cf866679b22012-09-12 07:09:35.368 UTCc44b9143-48dd-4172-b44d-6d39cb57b4212012-09-12 10:06:17.872 UTC9abaa51a-ea9b-480f-970a-812916f1c4a72013-02-04 14:49:09.919 UTCc7f596eb-b461-4a82-acde-e369c09d88062013-02-05 09:54:26.514 UTC92b312b4-d97a-4767-a54f-6d1e2ff411fb2013-01-28 15:17:26.598 UTC48c1a107-fc59-43a2-b40b-3193dbee96212013-02-04 10:34:10.48 UTC84d272a3-ab36-4aa1-ba06-e5d4be6ddaae2012-06-20 13:42:04.903 UTC25736105-7e2a-4169-a17c-f6df342feb912013-02-05 18:58:33.132 UTCf7d6584f-421e-41c6-b70c-bc019cf356722012-06-20 13:27:25.847 UTCbada19cd-999b-4c78-996a-a8cf435bc1e82012-06-20 14:43:29.27 UTCPurpose:
Currently, this workflow takes one SNP and a concept set as input, calculates the matching score between these, finds co-occuring documents between the query concept and the match concept, finds the concept that contributes the most to the match, and the documents that support this finding.
Author comments:
The workflow is in Beta stage. It runs, but needs more testing with different parameter settings. This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery.
2012-07-18 13:29:38.141 UTCe06f04ed-8f2b-43b6-b73c-0c1db8ecb2682012-06-25 11:42:30.855 UTC42cc0e98-a177-4766-ade6-c4f6b634c96c2013-02-05 11:21:37.942 UTCdd3d3cf8-5693-4031-94a2-688b70d8375f2012-06-24 20:57:10.828 UTC4c055cd0-f134-4be3-a41a-11aad85725e12013-02-05 20:20:00.52 UTC3a597170-9a73-40dc-822e-7411a48c84a02013-01-09 08:59:58.479 UTC6157699b-3fab-429a-a253-081473d7f7b92013-02-05 20:47:07.598 UTCc9ce92ff-38c8-4b8b-84bb-df60c09e705d2012-09-11 15:29:14.683 UTC081ca849-6a33-4ce7-807d-088976f280ff2012-09-12 12:36:07.673 UTC02cbb28d-4940-47c4-a45d-8579a2f91d5d2013-01-29 15:50:22.589 UTC38d29248-0454-4b55-baa3-d24fab456b1c2012-09-12 10:54:47.812 UTCbc2328b4-2251-49e7-92a3-63c971b773c72012-07-11 12:57:09.537 UTCf470d697-590a-4a5c-a5ac-0421a2a5779f2012-06-25 21:42:16.998 UTC21363a00-84f3-40e9-b676-4e5da44ee4b82013-01-29 15:46:43.251 UTC6c275f7a-163e-41ce-913a-1074939d1b4b2013-02-05 12:21:26.778 UTC6f2a1eb8-b131-4182-852d-a7c38065b6f52013-02-05 16:28:25.603 UTC0d0232fd-9c2c-4f97-994b-a7b4fade3aeb2012-06-25 12:46:15.951 UTCd415cfa3-3d04-4dd4-b1cb-b1c8658d5cc42012-06-25 10:06:26.773 UTCbabf573f-83d7-4304-a59f-f1d53a19c4cc2012-09-11 10:06:58.293 UTC349299f5-c1d4-41f9-a3c8-256fb4dedecb2012-06-20 14:50:32.447 UTC9a17df2c-d08c-4ad8-b70d-17c26b2b2e672012-09-11 14:57:41.380 UTCaaa51b39-b160-4e85-a78c-cf6387ff30732012-07-11 12:59:11.88 UTC5552b01c-5913-4fc5-908f-64bcb8b9f94d2012-07-11 13:48:59.422 UTCe6475d43-1bdc-4f31-a4b6-0d9642f617fa2013-02-05 09:07:27.795 UTC07e1051d-482b-431c-8bae-f8b65ec6a0a02012-06-25 12:47:08.190 UTCe90f9090-4f42-42c7-94a5-6296d92f7acb2012-06-25 12:08:23.148 UTC7471d9d8-88d1-4d96-9719-b347cd36c2ff2012-06-20 14:38:14.733 UTC8b9aed18-36d1-4f57-a885-b2a7c2bac8732012-07-04 08:59:08.521 UTCb8f53807-cfa6-40d1-acfb-9aa59d38fa742012-06-23 14:14:48.33 UTC724f40c1-2c66-4d0b-ab41-59eb2b0f83832012-06-24 20:54:25.360 UTC81c79d04-e062-47ba-a22b-ddec56289baa2013-01-29 16:09:05.655 UTCfe747322-34f8-42fe-9aa8-aa202d6c6be92013-02-05 15:32:38.623 UTC616f2861-9708-4254-8ead-11fd31cdefe52013-02-05 11:35:58.360 UTC33f1f0d9-6566-44e8-8ddc-7791fe15aee22013-02-05 09:17:15.885 UTC3edb70a4-e66f-4b96-8e12-3e440266e3752013-02-05 11:55:18.600 UTCe2ba0280-202b-4d6d-821b-b3539384e2372013-01-29 14:26:51.986 UTCe6603d60-cfc2-4dc7-a8e4-3fbd83af38792012-06-25 12:15:42.217 UTC460d423f-3f88-4e17-b7dd-738b95cb117e2013-02-05 09:57:02.845 UTC1c82a7ea-5d2c-401b-b2e3-39a7c86a68ab2013-01-28 15:34:16.371 UTC5ee6b306-17f4-4522-a9cf-a4f1fcc835782012-06-20 14:46:27.522 UTCab8c2488-f5c1-44c8-b5ec-719f624a8c412013-01-30 15:29:42.994 UTCaa90d89d-a8e4-4d82-b828-c038cf9422d12012-06-25 18:08:31.488 UTC5fb7380d-11e5-4b0a-baaa-c1f6a988070b2012-07-03 10:07:57.998 UTCdc4bff60-a506-43bb-8573-3ef97c0316d22012-09-12 08:11:11.792 UTC5a01765c-980c-4476-a60b-4eebb2a7d7e42013-02-05 09:05:11.428 UTC199ad955-4a64-4f3d-8afc-c4b1c2f9d08b2012-09-04 11:17:06.46 UTC42dc2b06-15db-4e11-8b75-3a0e1aa66e892012-09-12 07:16:20.526 UTC01bdae83-abec-4364-840c-27a1224cfbd92012-09-07 15:02:00.202 UTC644e2cd4-f219-4b7b-900a-a7b3f36bd9dd2012-07-18 13:29:04.78 UTC78a5bc98-afe7-49b5-a411-739894b618ca2012-06-25 11:56:37.177 UTCc84310b7-61d8-4111-a9d4-1cbbc70c27f52012-09-11 10:01:31.727 UTC2a2de5a5-0450-49bf-b68e-c8910124c45a2012-06-20 13:19:11.570 UTC438277ae-2f32-49b5-bfc1-9d92845351f22012-06-20 13:37:27.462 UTCf1fd209b-ec99-4713-b66b-b22e0d673f9f2012-09-04 11:18:48.47 UTCd8ede669-0d53-4bd1-9a37-ded1cdb5bb1c2012-06-25 12:03:27.734 UTC0d15cb49-d14e-425b-b2c1-d1a34ce4b6f92013-01-28 15:14:41.764 UTCf73d30e4-44c3-4265-921c-af28f7e121ef2012-09-11 15:01:15.447 UTCFind_co_occurring_doConceptID_111http://rdf.biosemantics.org/owl/concept#30926192013-02-05 20:01:52.834 UTCConcept ID for the input concept.2012-07-11 12:32:30.622 UTCConceptID_211Concept ID for the second concept.2012-07-11 12:33:12.79 UTChttp://rdf.biosemantics.org/owl/concept#42753602013-02-05 20:01:15.767 UTCCutoff_value0012012-07-11 12:30:25.642 UTCThe number of co-occurring documents to return.2012-07-11 12:30:11.639 UTCDocument_ID196149802013-02-05 19:51:47.955 UTCID of the returned document for which the two concepts co-occur.2013-02-05 19:51:31.314 UTCDocument_titleTitle of the returned document for which the two concepts co-occur.2013-02-05 19:51:24.400 UTCL-Glutamine-induced apoptosis in microglia is mediated by mitochondrial dysfunction.2013-02-05 19:50:31.116 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/ConceptRecognizerService?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" 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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" 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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 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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_titleab19809c-64de-48aa-b573-563d94dd784c2012-07-11 12:34:09.767 UTCe609f005-94e4-4f8c-b796-50f567459a972013-02-05 20:01:53.20 UTCa40a52c8-90c5-4755-a6c5-acae5f99b0e62012-09-11 12:53:08.81 UTCFind co-occurring documents2012-07-11 12:35:28.748 UTC234b78c5-66c4-4e83-bbe0-a21ec539a50d2012-07-18 13:24:34.655 UTC58b2cab3-cf9d-419f-b41a-241990b5bc212013-02-05 19:51:48.145 UTC739b02c1-fc07-41e3-b4e5-9a7174e4df7a2013-02-04 10:58:13.386 UTC856c7313-b7d7-4522-a152-bf4f5bf5830d2013-02-04 14:13:02.886 UTCCreator:
Kristina Hettne
Contributors:
Web services by Reinout van Schouwen
Additional annotations by Marco Roos2012-07-18 13:23:59.195 UTCd42b0294-a5cf-4cfc-9635-26486e6139342012-09-04 11:17:59.103 UTC3beae759-c94b-45ff-99ab-d5471960ec112013-02-04 14:11:28.416 UTC6c42e1a2-7aec-4169-a712-79b6cf0729372012-07-11 12:36:19.218 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 UTC324bd118-08c0-4cc2-a3cf-86a0a6d802e02012-07-11 12:39:06.872 UTCGet_concept_informatConcept_ID00http://rdf.biosemantics.org/owl/concept#30926192013-02-05 19:57:02.768 UTCConcept ID of the concept to retrieve the name for.2013-02-05 20:06:06.218 UTCConcept_nameThe name of the concept.2012-07-04 11:51:39.675 UTCGLS22012-07-04 11:55:50.464 UTCConcept_IDhttp://rdf.biosemantics.org/owl/concept#30926192013-02-05 19:56:21.234 UTCgetConceptProfileparameters0parameters00This Web service returns the concept profile for a given concept ID.2012-09-11 12:51:04.847 UTCnet.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://ws.biosemantics.org/ConceptRecognizerService?wsdlgetConceptProfilenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetConceptProfile_inputconceptId0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivityconceptId0'text/plain'falseoutput0'text/xml'0<s:extensions 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_ID3afe257a-1246-4267-be82-ccb4203af53f2013-02-04 14:49:02.214 UTC0f9f0834-7609-4af4-b3dd-6a9452cda1232012-09-11 12:44:40.991 UTCGet concept information2012-07-04 11:53:15.951 UTC4b5150df-f12d-4f9a-a51e-a655e4c3cba12013-02-04 14:41:45.41 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 UTC80bc71ed-b511-4824-98e2-3e5add19aaae2012-09-07 14:29:24.729 UTCcefac9de-143f-47d7-b318-2af786d920462013-02-04 14:52:58.669 UTCc6eaa639-5ee7-474e-9dbb-401927d650302012-09-11 12:49:35.323 UTCcf644a3e-3942-4c42-b8c7-2f834fd110d42012-07-18 13:22:54.983 UTC2824bc65-af91-41c0-8912-e24151314a572012-09-11 12:51:06.419 UTCd9f930cb-1c79-46de-9935-e97cc62f5df72013-02-05 19:57:02.921 UTCb31a4602-eda2-485b-ad82-07db5fe820682012-07-04 11:54:39.48 UTCff59aa50-8acd-40d6-b6dc-042b289db3142013-02-05 11:10:08.41 UTCa2ecda87-b5b6-473a-af29-b9fcf32ea7072012-09-11 12:40:55.902 UTCdea60608-70c7-4cf0-a8da-8513eb1a440a2012-09-04 11:17:36.783 UTC04d2b539-0ecf-47a2-b036-73e97581556f2012-07-04 11:56:13.312 UTC83c3dad7-8d79-44e4-959a-e01ab677a6452013-02-05 20:06:08.228 UTCExplain_concept_scoresC_ConceptID00The concept id of the C concept.2012-09-11 09:01:25.824 UTChttp://rdf.biosemantics.org/owl/concept#22631262013-02-05 20:09:11.301 UTCcutoff00Maximum number of explanatory concepts to return.2012-09-11 08:30:14.173 UTC12012-09-10 15:18:30.889 UTCA_ConceptID00The concept id of the A concept.2012-09-11 09:01:33.736 UTChttp://rdf.biosemantics.org/owl/concept#30964312013-02-05 20:09:19.271 UTCB_ConceptNameFADS22012-09-10 15:17:05.627 UTCThe concept name of the explanatory B concept.2012-09-11 09:01:44.136 UTCB_ConceptIDhttp://rdf.biosemantics.org/owl/concept#30964312013-02-05 20:09:37.980 UTCThe concept ID of the explanatory B concept.2012-09-11 09:01:40.385 UTCB_ConceptContribution43.362328410148622012-09-10 15:16:19.600 UTCThe 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 UTCexplainScoresStringInputparameters0parameters00This Web service takes two concept ids as input and returns the top ranking "B" concepts according to Swanson's ABC model of discovery, where the relationships AB and BC are known and reported in the literature, and the implicit relationship AC is a putative new discovery. It might also be the case that AC is already known. In that case AC does not represent a new discovery but will still be returned by the Web service.
The concept contribution is also reported by the Web service. The concept contribution is the percentage of the contributions of the individual concepts to the coherence score (the average of the inner product scores of all possible concept pairs within the group).2012-09-11 08:57:10.939 UTCnet.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://ws.biosemantics.org/ConceptRecognizerService?wsdlexplainScoresStringInputnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeexplainScoresStringInput_inputcutoffValue0conceptCUIsAsString0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivitycutoffValue0'text/plain'falseconceptCUIsAsString0'text/plain'falseoutput0'text/xml'0<s:extensions 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_ConceptContributionPurpose 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 UTC89f2da6a-161b-47b1-a048-a65fd35f912c2012-01-06 11:47:16.46 UTC8efd062c-22d8-4fc6-bfe4-ea8f96ba7e2a2012-04-16 12:58:21.8 UTC7a995f89-0c37-48b9-b0f7-8eca5cd364202012-01-06 11:51:06.790 UTC4bed166d-9815-4a35-a613-869b300b79732012-04-16 13:04:34.678 UTC13050a9d-bdda-4de5-8bc7-8503457302cd2012-04-16 13:02:36.340 UTC8d4a9091-0ba9-468e-9883-7b08e5212cd22012-04-16 13:07:32.864 UTC7d6ba6db-2552-4c15-b800-1789f5385d442012-09-07 15:18:14.352 UTC90f0af1e-a653-4a85-889c-4120accdd9d92012-09-07 14:44:36.440 UTCabaeb048-e186-4c8d-92d4-6b32b22603d82012-04-16 13:01:16.427 UTC3c6eca00-e3a8-46b8-86bd-7c4b48a3ac772012-07-18 13:20:01.872 UTCfc7ae322-fcac-41c5-b136-0767d52680b02012-03-21 13:53:26.66 UTCExplain concept scores2012-04-16 13:00:42.27 UTC4b937a61-6180-48ce-a679-cf3ed1c8f2082012-09-11 08:58:54.136 UTC4f826cfe-3950-4151-bbe6-bff67413be512012-09-07 15:22:15.103 UTCCreator: Reinout van Schouwen on behalf of the BIoSemantics Group
Adaptations by Marco Roos and Kristina Hettne2012-09-11 09:02:52.112 UTC713fa342-cdf4-48b7-850d-abecb37b9b1f2012-09-11 08:58:13.328 UTCa6c096b8-050d-48bf-8b9c-114762aac26d2012-09-07 14:52:03.90 UTC2b762f5e-4473-4d48-b78f-df306600467a2012-09-11 09:11:13.838 UTC6bab82da-54d0-4bc7-96fd-e5c5d3c6d77f2012-09-07 14:37:53.808 UTC88e1d0d3-3377-4a21-a98f-19020444e6862012-09-07 14:58:20.922 UTC0faa8a91-3a1c-4e03-b74d-f271e7b962902012-04-16 12:55:56.499 UTC9e4c2fcc-6dcc-46d5-9edd-d7841389ef5c2012-04-17 08:22:27.551 UTC9a6508bd-87c3-4d9c-99f2-9003b5b57df42012-09-11 09:01:50.31 UTC1ea652c5-572b-4b0a-b66d-5ae41a7b7fe12013-02-05 09:41:27.678 UTCa260c127-7bbc-4dde-86a9-80647fcbb8622012-09-10 15:18:42.957 UTC09802e77-93ac-45ba-9ad5-e7bea33cda8b2013-02-05 20:09:38.174 UTC2b5167d3-3864-46c1-b761-b66ab721da542012-02-03 13:52:44.748 UTC541a7a2d-e3e3-490d-885b-52d653a21d112012-02-03 11:42:15.89 UTCbb8d1d77-e3d2-4cee-aee9-3cd4e1bd85472012-01-06 12:38:00.681 UTCc416805f-aa9d-4d44-b434-f253935ed0ef2012-09-11 08:57:11.33 UTC8f284446-2578-4c4d-b81d-e842a463641b2012-09-07 15:34:00.455 UTC142a2c6d-8e96-4c9f-ad64-da97fd4c25972012-09-04 11:16:44.759 UTCGet_concept_informatConcept_ID00http://rdf.biosemantics.org/owl/concept#30926192013-02-05 20:07:38.791 UTCConcept ID of the concept to retrieve name and definition for.2012-07-04 11:50:31.405 UTCConcept_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/ConceptRecognizerService?wsdlgetConceptProfilenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetConceptProfile_inputconceptId0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivityconceptId0'text/plain'falseoutput0'text/xml'0<s:extensions 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_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_name3afe257a-1246-4267-be82-ccb4203af53f2013-02-04 14:49:02.214 UTCb31a4602-eda2-485b-ad82-07db5fe820682012-07-04 11:54:39.48 UTC04d2b539-0ecf-47a2-b036-73e97581556f2012-07-04 11:56:13.312 UTC80bc71ed-b511-4824-98e2-3e5add19aaae2012-09-07 14:29:24.729 UTCdea60608-70c7-4cf0-a8da-8513eb1a440a2012-09-04 11:17:36.783 UTCcf644a3e-3942-4c42-b8c7-2f834fd110d42012-07-18 13:22:54.983 UTCCreator:
Kristina Hettne on behalf of the BioSemantics group
Contributions:
Web services by Reinout van Schouwen2012-07-18 13:22:40.527 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 UTCa2ecda87-b5b6-473a-af29-b9fcf32ea7072012-09-11 12:40:55.902 UTC0f9f0834-7609-4af4-b3dd-6a9452cda1232012-09-11 12:44:40.991 UTC6a41503c-d915-4eac-998e-0d10ee8f32f12013-02-05 20:07:44.871 UTCc6eaa639-5ee7-474e-9dbb-401927d650302012-09-11 12:49:35.323 UTC4b5150df-f12d-4f9a-a51e-a655e4c3cba12013-02-04 14:41:45.41 UTCSNP_ID2EntrezGene_IDSNP_ID00rs26578792012-07-16 14:27:52.745 UTCUse (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 UTCset_width00The allows the user to set the flanking width for the gene for determining SNPs.2012-09-11 11:08:34.646 UTC1000002012-09-11 11:08:43.702 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_IDe7471436-942d-4d3e-98b2-65e15995183e2012-05-28 16:15:51.854 UTC1e2fc50e-6f54-4c4b-854c-aecf80d242722012-05-23 09:11:52.877 UTC4c1c8924-c2c3-4410-bf73-5db2e44359982012-07-09 14:51:20.747 UTC59c48ad2-46fa-4c6a-920e-35585a726e7f2012-07-13 12:50:51.21 UTC821e379f-0aaf-4220-8d6c-83517950317f2012-05-25 15:10:34.774 UTC537f3d64-b1fd-43bd-9c13-ad4372dd7a512012-05-29 09:49:35.836 UTC8c5e8e26-1959-47e8-931a-f3d6053545242011-12-04 20:25:27.361 UTCa8ff4a9e-1161-41d9-b903-4d1fd1fd25e42012-05-29 09:13:08.665 UTC9d84acd8-2d53-46c1-b1d0-d395b26d5ffc2012-05-25 14:14:15.364 UTC892ce0b4-fffd-4962-a850-445e2afe54c92012-05-28 14:26:47.563 UTC9916b6e6-526d-4583-b390-64518c4f06a12012-07-13 03:37:35.435 UTC720aa582-de73-463d-b2bc-ddd1699ebc4b2012-05-24 06:55:01.111 UTC37852792-3988-4ca1-894b-f18c3e6caa3d2012-05-28 13:36:48.449 UTC909dac87-86fa-4b27-b8f0-e58b6acf03292011-12-02 20:03:51.11 UTC470b1948-bcb8-401e-88ee-72172c9a1c752012-05-25 14:15:48.972 UTC56ab1507-d44d-4569-b627-7984fe3da0aa2011-12-05 08:55:56.457 UTC6dc63288-570b-4c6f-9d1b-3018852941bf2012-05-24 14:32:15.752 UTC0d757f59-9497-426a-b0dd-bdb68d3796d02012-05-24 11:52:38.509 UTC98b01cc5-cc3c-4a1b-b6bb-cc4e69c053402011-12-05 12:35:10.779 UTC07f68d25-cfa2-431a-a66f-7f30ffbef86c2012-05-29 07:46:27.651 UTC7732d491-9163-41d3-b43e-07f5e3710a5b2012-07-13 03:45:40.363 UTCf02a8cf2-7757-4252-b5ac-ad6729f9d80f2011-12-05 08:51:49.367 UTCde5376be-26df-4424-82f6-735797ecbb4d2011-12-04 19:54:39.289 UTCd7cc4df4-9383-4543-870f-1beaa09c70f72012-05-29 10:05:40.594 UTC681bb15e-0cb0-4d46-b94d-50c8af23d5822011-12-05 10:05:00.123 UTC0fe8a23c-ab84-4025-a5c0-27c652d9b7eb2012-05-28 15:06:02.685 UTC57237b54-36f7-4a2c-9833-4ab73bf3cea92011-12-02 20:06:32.660 UTC65969e5e-369b-46b3-88d7-22747d38898a2012-05-29 09:14:34.991 UTCc6a4b654-7519-49bf-bb26-82fd81e32d522012-05-28 14:47:56.177 UTCaa1e05f9-bef7-4a1e-9137-f9a139fc63282012-05-28 16:17:11.384 UTC9052cca1-3bac-456e-8964-bc5a97f24e122012-05-23 09:47:46.18 UTCb997e938-3b2d-4ac3-a0ec-b90fa5ecfb862012-05-24 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13:28:40.258 UTC7ffb408f-a8d9-4937-a761-0de05f695aee2012-05-28 13:15:23.516 UTC4717b80f-c414-4cef-a833-5c74344454812011-12-04 20:17:49.522 UTC0550476f-da31-4066-b14f-f5f483f232fa2012-05-28 13:12:01.864 UTC49cf34cf-c5c0-4623-bf73-4a16d0750f9c2012-07-12 23:18:21.867 UTCfc7d0b18-95da-435a-a49c-bd4957d019292012-05-28 13:22:58.144 UTCa3dc86e8-ceb9-4224-a702-83ef11cddaa12011-12-02 20:12:19.143 UTCc65a9a3a-909c-42a3-83cf-edd32d2e7aa92012-05-23 09:39:51.321 UTCdf724031-6ef9-4bbf-80d1-0978f512f1662012-05-24 07:13:09.787 UTC400ed11a-24fd-457a-a9b7-cc3ef85e8ad72012-05-24 11:44:12.16 UTCd22656b0-2793-4ba7-8f90-1f80c27d54132012-07-10 12:46:34.516 UTCbb845add-ef95-4621-ba20-7cdbcfd8895c2012-05-28 14:30:06.480 UTC323b72ad-2dad-491c-adcc-4b01f61d15c52012-07-13 03:48:12.471 UTC6d2380e8-5477-48e8-9ed1-c82d71a347fc2012-05-24 11:32:30.203 UTC45f3551e-d015-4ca6-b0df-e1607fa965b02012-05-28 14:22:00.164 UTC773ad5ff-fa77-4807-9699-bc75f0be63b92011-12-04 19:55:52.32 UTC3e9f3842-9dfc-4b71-a356-a1516667a0652012-05-28 16:29:16.964 UTC663775b4-68ba-4dfe-8aa3-2a079a61805c2012-05-28 13:17:48.527 UTC799b2c7a-749d-4e85-96b8-57d4ce9d49a82012-05-28 13:49:09.988 UTCc98b52f2-07a9-41c1-93e2-537baaca690f2012-05-25 14:45:00.606 UTC1f9fa403-1de0-4605-ae95-7964bb2b2a912012-05-23 09:00:46.292 UTC2082c444-8dc5-491d-98f0-a38e48f14ad22012-05-28 14:58:09.975 UTCbd87bc54-b86c-48c1-9bcc-0d943cad671e2011-12-02 19:52:46.244 UTC5b0b16b2-6159-4a45-8f0e-e61e52a42ed02011-12-05 12:50:24.222 UTC63da0a3f-eb7a-4b96-a50f-476d09f0f6b82012-05-24 10:14:07.658 UTC8481be24-7358-4c81-a8fc-2b2b89f0069e2012-07-14 03:17:33.803 UTC122b2bb9-fdc0-4545-a673-487ec8eb4c9f2012-05-28 13:32:55.580 UTCe2cf19ae-7516-4842-9c8d-7243da52e6fd2012-05-28 13:23:25.66 UTC594f53e9-a4fd-422b-b11a-c95aeae12f6b2012-05-25 14:18:14.345 UTC3105f50e-deab-4464-8ac2-ab81746a8e1a2012-05-28 15:01:00.409 UTC5d768f1f-89a3-4e49-8852-f00f1870d3352012-07-18 13:09:23.517 UTCc14f091a-a1b6-43a6-af28-7599b1ddd8b12012-05-24 07:08:23.312 UTC2ce8d6ce-78ef-4ba3-93f3-ae418cb04a042012-05-24 11:37:44.705 UTCf6370d45-5817-4828-98e5-8fa459e528762012-05-28 13:30:49.145 UTC33f3d4e3-80a9-44ec-8cfb-f84ebc21051c2012-05-28 12:44:30.573 UTC78067d1f-1fb1-404d-9494-50154802f9d92012-07-09 14:24:55.244 UTC07448a4e-6711-403d-80a7-bbce3a10c9e52012-05-23 10:24:50.354 UTC8a7d22d5-e9ba-45b8-b0dd-017cb62649f32012-05-24 06:48:16.752 UTCb594a08d-11fc-459b-9243-491bd5c0feda2012-07-13 03:03:20.745 UTC68edacf2-b990-4a31-b694-c8cacd99e4652011-12-02 20:18:54.225 UTC8a72c4e8-34e8-4850-99d8-7edfef99eb592012-07-10 16:28:46.151 UTC5feed474-e086-436c-9dc8-547e6f6648bc2012-05-25 14:20:34.984 UTCa8e9dc49-d486-4d55-a5a2-8de2e51149ea2012-05-24 10:16:40.525 UTCb31c16f3-c7f3-4f45-8808-dbcca22867612012-05-28 13:50:16.908 UTC8ed5c836-7421-4937-82a4-afd071d360682012-05-28 15:49:27.444 UTC52aa7823-c531-4e64-9543-bbf57aa4c0de2012-05-24 13:30:11.840 UTC7e4d6ec1-007e-41b3-9b1a-39923c3843b62012-05-23 08:54:08.937 UTC6ee5dac9-47db-4acf-8de3-4baf71ac2e0e2012-05-24 07:12:27.913 UTC225c56b9-df03-416e-bfef-ba2eb57a22cc2012-05-24 11:45:35.231 UTCe9205450-f061-4220-a690-24780f5752582012-05-24 10:09:38.171 UTC16fc0fde-d715-4380-8c10-4f4362d71ac82012-05-24 14:14:29.971 UTCf0b2d523-78cc-49db-88a3-3c93c837b5fb2012-05-29 09:17:34.988 UTC8b1ca805-f1a3-45c0-8dd0-c2367fb624942012-05-29 09:24:10.559 UTC7b6b6168-7421-4b1a-93e6-b6903bf56c492012-07-13 04:55:09.867 UTC136247cc-6e2d-4a2c-a703-590419195f992012-05-29 07:49:50.399 UTC9a5c4eb2-c8a0-4ab5-8733-2919f7a29c672011-12-04 20:23:12.582 UTCc23caeac-180a-417b-b101-afa124068d222012-05-24 11:18:13.132 UTC5579e4f5-3b8a-41b5-a0b9-5a73d4d8f8b82012-05-28 15:22:26.463 UTC65737da5-8b7f-4f23-88ab-d2da3ad8cd9e2012-07-09 14:26:27.567 UTCb8ca8ea8-4261-47cf-826e-005f5d9658832012-05-24 11:42:23.255 UTC7c853e04-989f-467d-960a-8ad72355c5f22012-05-29 09:56:07.94 UTCba6ce7ea-bec1-4cdc-8c9d-bae2d1086a9d2012-05-24 10:04:37.281 UTCd53f5b51-874e-4b1e-809f-b66e9663cf8f2012-05-28 15:41:56.31 UTC365e4908-2036-409a-96c8-ce2adb53049d2012-05-24 11:19:45.535 UTC3e653fd3-19df-4ad7-b46b-a47192bf66392012-07-13 03:09:16.430 UTCc5bd0205-5369-43d1-99b8-97d96b84f5152012-05-24 10:25:41.575 UTCe489f882-ec1f-492a-b233-89afc3a5d9982012-05-29 08:19:59.344 UTC4a0e6451-c4f7-4f7c-8865-ccecc158cde22012-07-16 14:22:28.219 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 UTC4002f6bd-d804-4219-bf5d-1e3da51e388d2012-07-14 02:58:10.79 UTC0aaa6f86-7652-4191-91b9-933364dc640f2012-05-28 13:39:00.742 UTC9df76bf6-9c7e-47b3-bb5a-aadbcde0902c2012-05-29 10:01:12.633 UTC78bad41f-3d43-4052-9e7f-5619cb2866bc2011-12-02 20:20:22.944 UTC0f479371-ee41-44bb-b265-76c85e6596532012-05-24 11:30:53.380 UTCe33d1b5a-4387-40af-8eb3-610183d068a12012-05-25 14:48:46.775 UTC25b6de5f-396f-45c9-aaa2-e3277851f2c22011-12-05 09:29:51.46 UTC6cba3d8f-b595-4757-8de7-d6c413032b292012-05-29 09:57:51.420 UTCf3fd6d4a-3b5a-4b82-a980-54ffd3b55e7b2012-05-28 14:23:40.396 UTC42a8db21-13e9-427a-9ed4-3ec73e5d09ad2012-05-24 10:18:21.504 UTC343ea31a-d25d-40e2-9d94-bb10630333392011-12-04 21:31:09.853 UTC51b686d7-a903-449c-b10e-789e3eacaa772012-07-13 12:02:05.16 UTC79dc3865-dde2-4c84-88e4-3069af4193632012-07-13 20:26:29.179 UTC880814c1-426f-4e59-8882-9241af4421492012-05-28 15:50:25.224 UTC689a09b4-747d-4616-8bea-f7d4c9cfad1d2012-05-29 08:00:06.553 UTCc3eb4a90-1ef2-405e-8f56-e6f6ec2f87db2012-05-28 15:46:04.713 UTC86aae19c-517c-4f16-a964-4031ae65dcb22012-07-13 19:05:49.202 UTC1b31e1dc-c604-41cd-ada0-7a630d9ab2022012-05-23 09:50:23.48 UTC396f1052-af35-4b0c-b81a-e6c80c9aa79b2012-07-13 04:53:30.495 UTCc43d0c46-4007-4474-a96e-17f9e6f946232011-12-05 12:39:09.738 UTC9754d989-1173-40df-bed9-a561f2c102c52012-07-13 11:32:04.849 UTCd5acc483-c168-468a-b09f-aa0e5bdd691e2012-05-23 09:20:31.391 UTC68b6a3a4-b582-4e29-9b7f-29c44c5c265b2012-05-28 13:32:12.424 UTC7dfa4a0e-911a-49e7-8fa9-867599fe1acb2012-05-28 14:13:25.228 UTCc6954af8-29d3-49f2-9034-38847f1dd8902012-05-28 14:28:31.311 UTC9392534b-c27e-4185-9572-110f7d720aa32012-05-29 09:29:57.333 UTC16ea68c5-c95d-4d0e-b08e-ea5c296e1ab32012-05-24 07:16:16.281 UTCd80fb6b7-8bf4-47e1-8f44-2a03441e85662012-05-23 09:22:12.952 UTCe8e28dad-160e-438f-b1a4-1bc0c952cee42012-05-29 08:10:33.77 UTC2ff5f42c-ad5d-4855-afb6-994d95b56ad52011-12-05 12:45:17.858 UTC8dc439f6-ae2e-4484-9f61-d5913cbbc83e2012-05-24 11:21:29.155 UTCa4414467-dc1d-49ce-9f35-ee643b2b0a922012-05-24 07:40:13.121 UTC58640859-5834-45bc-8133-a44a208b0b222012-07-09 14:41:53.348 UTC162f2322-5cc8-4872-992d-154c488ae2be2012-07-13 11:06:07.271 UTC67bf7e76-47ea-4757-9d02-de763fba160b2012-07-13 11:25:00.588 UTC4ed47709-f143-454e-9df8-fc1ee053577c2012-05-28 14:45:04.634 UTC9e402cfc-fd28-4555-b7a0-75cb8851a8232011-12-02 20:02:17.831 UTC2e5e5024-9bf2-4adf-befb-f4585fe28e0e2012-05-24 10:11:45.87 UTC404b5061-dcee-4022-af0b-3f03ffb579d92012-07-10 13:47:51.897 UTCde94784e-ff3b-455a-b46d-115a3425f8702012-07-12 22:58:00.866 UTCf961460c-2aac-418a-82c8-c6f9bb84bc252012-05-23 09:33:23.569 UTCf651a96e-f829-4d2c-812e-04b9147995272012-05-24 14:16:55.168 UTC8fba433b-1a50-4c58-9d88-4ce23c30b3ab2011-12-04 20:34:38.768 UTC82caace9-db1a-4b08-8528-7fed9f4fe3e32012-07-13 02:54:14.662 UTC72797bde-afec-453a-831c-bc752526ec9b2012-07-12 22:54:04.805 UTC55699458-d13b-44c4-88a3-00b9a94d4bfd2011-12-04 20:29:57.352 UTC3b268f07-e232-491d-874d-fdcb50b1210f2012-05-24 06:49:32.736 UTCaa106f23-15fa-4bde-8481-f38d9145ea4a2012-05-28 15:24:47.801 UTC418d93b2-546c-4e33-b77a-9ef284b183922011-12-05 09:21:49.671 UTC6a975b77-984e-4396-92f0-74aaba68cc6e2011-12-05 09:26:42.234 UTC43260d53-f13f-4b02-8755-96eb198c7a132012-05-28 13:42:07.264 UTC934a7783-3866-49c3-be45-9f6c00f25f042012-05-28 13:42:43.45 UTCd7b84de5-d36a-4090-8ab4-d37dde019b322012-05-28 14:18:44.466 UTC56f48acf-de19-4709-991f-cdc768c578d82012-07-09 14:15:50.905 UTC3d9a2e4e-9eaf-46ef-ac71-9ba04a52c4ba2011-12-04 20:51:57.350 UTC08489858-3622-42b4-8645-a7508a5a7eea2012-05-24 11:49:05.799 UTC12676d8e-8e07-44a8-adc3-246bed5f719e2012-05-29 09:38:49.885 UTCf4bbc070-c3f5-48c7-bc3b-3e36572e755d2012-05-28 15:21:02.683 UTC56d2388f-4512-4039-8ac5-3765096581562012-07-10 16:26:23.285 UTCe2e11b86-8b2e-4567-8da8-f508470a72062012-05-24 10:05:09.857 UTC87ea0a35-0f9e-4fdb-bf4f-29dafeab759e2011-12-05 09:20:36.359 UTCb6009e1a-5bd6-44e3-bdd6-9af7c90bdc522012-05-25 14:17:37.221 UTC442fbd70-6edc-4aac-a52a-1e28af3918832011-12-02 20:21:29.89 UTCcdf314f3-c07d-4299-9f12-b2fb34f16d712011-12-05 10:24:34.417 UTCf2dd9a4a-91c0-4c6a-aff4-43041ef6f4af2012-05-24 10:07:59.36 UTCeedbb948-296f-448a-baec-81e9fe57a61f2012-05-24 06:58:44.89 UTCeeaad7ea-4fbd-4283-b58f-68f1e9bb2a3c2011-12-05 10:12:47.595 UTCec2bec87-7bbf-4e50-a8c6-86a2aac5435f2012-05-28 15:30:15.216 UTCc70559bc-32ea-45d5-9e0c-5c165efb1dce2012-05-29 09:16:03.115 UTC93602cc4-585d-434c-99f1-de25ffa087712012-07-12 23:08:39.267 UTC44ce7b0d-aacc-4d8b-a074-befeb5e37ad52012-05-28 13:44:39.89 UTCe5e29e4d-d497-493a-9860-a8bd8d5657542012-05-24 07:11:13.72 UTCSNP_ID2EntrezGene_ID2012-07-16 14:26:57.243 UTC92b50465-c47e-4f10-959f-6ac4ea4120692012-07-13 10:53:40.120 UTCd2fab0b4-1886-49e3-b4e0-2ef4791554e32012-05-24 14:28:23.199 UTC815b4de2-2533-4c65-acc1-61570ff0b7db2012-05-28 14:46:29.632 UTC8369db6a-1d67-44e8-bdc0-5586d6ac26652012-07-09 14:27:40.403 UTCfe69338b-803c-4d67-9aaa-b8710bd723172011-12-05 09:02:50.152 UTCbba91acb-8f29-45c8-b827-5fa8573f354d2012-05-28 16:08:22.706 UTCe1852394-62d4-4ebf-b574-803b0a8e92762012-05-24 06:52:22.865 UTCAuthor:
Harish Dharuri
Contributor:
Kristina Hettne2012-07-18 13:06:17.451 UTC5041e588-5b2c-46e2-bcd5-6df40c41b9852012-07-13 10:56:58.41 UTC32012e67-9983-4358-b01f-36b0cc8a7c732012-07-16 14:30:23.715 UTC98a34165-cf45-4fbb-92dd-9714728b200e2012-05-28 15:34:06.993 UTCbccb19ff-4ec7-48a0-ac70-c04c1b1c0ad12012-05-24 10:21:12.433 UTC5267ab5b-b2c3-4b51-b145-616fca8833132012-07-16 14:28:00.556 UTC225e0718-30f5-4431-9c93-1367d0875f1c2011-12-05 08:42:08.453 UTC178f4858-1d1d-4749-993b-5c50c35fce9e2012-05-29 09:34:11.328 UTCba3d90fe-3286-4a20-9f70-1f96d3553cde2012-05-25 14:43:53.153 UTC18633aad-72f8-4de7-8355-7a3b41d2e7822011-12-02 20:01:21.139 UTC0dd472cc-fca4-40c7-befc-dc40d070613e2012-05-28 12:57:45.369 UTCc79e9515-71ad-43a9-aaa5-b3c0b9f0c8442012-05-23 09:32:11.351 UTCf894d03f-e142-475a-91e5-d97606dde2762012-05-23 09:13:55.875 UTC74431655-80e2-4cf3-b348-6b63f016e5f32012-07-13 19:10:56.745 UTC4c18297b-d76f-494c-8e02-db4f29a0bb0d2012-05-29 07:52:34.240 UTC4f478714-44cb-4f1a-8f6f-93b7153386e52012-05-28 15:14:57.799 UTCe30dc445-e2a0-43f3-bfd7-083d248b55da2012-05-28 13:40:30.818 UTC21f88381-9624-4b53-b90d-338c897666402012-07-12 22:31:49.351 UTCb32a03e5-3a55-4c72-b3f5-5f041d859d252012-05-28 13:43:41.246 UTC4df0a34f-79f5-4db9-8139-c816c4e8dca42011-12-05 08:57:23.769 UTC2df74fd6-bad1-407a-96ed-5d789a5d790d2012-07-12 22:38:14.266 UTC6fafb7ef-e8da-4d79-a359-a589a488844a2012-07-18 13:06:30.71 UTC04371b1b-18bd-4405-a82d-c3db639977a02011-12-04 20:35:38.750 UTCd60af604-f923-4b3b-84a1-e5cab6eba64f2012-05-24 10:23:12.911 UTC9c66acfa-bc51-4c4a-aea4-52bbd719b3ee2012-05-28 12:55:01.606 UTC1a15a664-74ff-430c-8c5b-9a44b75c5d922012-05-24 10:24:32.110 UTC8b743d45-0ed3-40af-b86c-621a622becd72012-05-25 15:13:17.443 UTC50e39586-05d0-4cac-80e5-ca7476e4c62c2012-05-28 13:06:09.328 UTC1db5c6f1-a905-41a5-83c8-d8f79cd16ffd2012-05-28 14:17:31.656 UTC509480d2-5e56-46b9-a210-e1abd7f4fd592011-12-05 09:36:01.703 UTC39ebc55b-a839-4ddb-854b-ff51dc3777032012-05-28 14:11:19.840 UTCc0b817e8-664b-4f21-8737-6cdde6c33e722012-07-13 20:13:19.177 UTCbd0e27ad-006c-4572-bfba-39fb8ce0d5f72012-09-11 11:10:37.403 UTC9dbddb98-bc13-49e4-99ea-abadf243ba482012-07-13 12:18:30.623 UTC819a2da6-ac2f-450f-8898-ca47c9e176902012-05-28 13:26:14.402 UTC354bd383-3970-46e5-a69d-756f249db3fd2011-12-02 20:06:00.39 UTC1f39dd51-fbda-49c3-b718-aeb0ff17961f2012-05-24 14:39:02.624 UTC3173b7fc-97e4-43c3-9494-e09ca7ab00092012-07-13 20:07:19.961 UTC9fa557e0-a81d-4bb4-9f0f-1cbdfe7cc68e2012-07-13 03:11:34.351 UTC3b8a830b-befd-4274-a627-de73d272b6f82011-12-05 10:11:10.661 UTC01b0a1c2-2ea1-42fb-8f77-3102cb2029c32012-05-24 08:02:12.628 UTC388cc1a4-6e6d-4f55-b250-6783360f073d2012-05-28 13:27:42.744 UTC03b1577b-a1c9-4311-9e93-8297c6d544452012-07-16 14:23:43.831 UTC09ff0ed8-017f-41e2-a5ac-8b25a86d18962012-05-24 07:14:01.348 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 ConceptSet (a list of concept identifiers) to be queried. For example: 42753602012-04-16 12:39:57.499 UTChttp://rdf.biosemantics.org/owl/concept#42753602013-02-05 20:12:35.528 UTCMatch_concept_IDConcept ID of the matched concept.2013-01-29 14:25:01.866 UTC<http://rdf.biosemantics.org/owl/concept#1156814/>2013-01-29 14:24:54.220 UTCSimilarity_score0.00161509089237915842013-01-29 14:25:31.229 UTCList of similarity scores for the matched concept profiles.2012-09-11 12:29:44.886 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. A list of IDs for the predifined concept sets can be retrieved by running the List Concept Sets workflow (http://www.myexperiment.org/workflows/2999). The example ID corresponds to the concept set GO Biological Processes.2013-02-05 20:18:25.345 UTCnet.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://ws.biosemantics.org/ConceptRecognizerService?wsdlgetSimilarConceptProfilesPredefinednet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetSimilarConceptProfilesPredefined_inputcutoffValue0conceptSetId0queryConceptProfileList0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivitycutoffValue0'text/plain'falseconceptSetId0'text/plain'falsequeryConceptProfileList0'text/plain'falseoutput0'text/xml'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getSimilarConceptProfilesPredefined" name="parameters" qname="{http://services.conceptrecognizer.lumc.nl/}getSimilarConceptProfilesPredefined"><s:elements><s:basetype optional="false" unbounded="false" typename="int" name="cutoffValue" qname="getSimilarConceptProfilesPredefined>cutoffValue" /><s:basetype optional="false" unbounded="false" typename="int" name="conceptSetId" qname="getSimilarConceptProfilesPredefined>conceptSetId" /><s:basetype optional="true" unbounded="false" typename="string" name="queryConceptProfileList" qname="getSimilarConceptProfilesPredefined>queryConceptProfileList" /></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.InvokegetSimilarConceptProfilesPredefined_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="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" /></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.InvokegetSimilarConceptProfilesPredefined_returninput0SummedSimilarityScoreList11MatchConceptProfileList11net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivityinput0'text/xml'java.lang.StringfalseMatchConceptProfileList1l('text/plain')1SimilarityScoreLists0'text/xml'0SummedSimilarityScoreList1l('text/plain')1<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="true" unbounded="false" typename="matchingResult" name="return" qname="getSimilarConceptProfilesPredefinedResponse>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_scoreAuthors:
Kristina Hettne, Marco Roos
Contributors:
Reinout van Schouwen2012-06-24 20:56:28.572 UTC7986f41c-7556-45d9-bcb3-f557b69f3acc2012-04-15 20:28:43.911 UTC487ca7a4-63fa-45f9-baab-8f9a053ca9d02012-04-16 12:50:38.225 UTCda482794-4042-408d-adc4-c035dcb831ab2012-04-16 12:41:12.260 UTC8bdb17e0-10d5-42c5-9649-595b5b3ca2262012-09-04 11:16:15.351 UTC0d2ee2ad-e803-4529-afc2-e15bcd124a0c2013-01-29 14:14:04.577 UTC4d330136-ca78-4fa0-ad95-0d34b85f8a762011-09-20 15:56:44.26 UTCfafb8d94-026f-4044-b3ce-866fc199229b2011-09-28 12:06:54.60 UTCe7d32565-d838-4bd0-987d-f03c4093d3452013-01-29 14:21:26.174 UTC9a1764af-8145-4c13-a849-38a031e6f2dd2011-09-28 12:26:45.132 UTCabf2582f-e23f-40ff-b26a-c51da6f9e8f52013-02-05 11:11:56.753 UTC4eb7b1fd-ec11-4fff-8a9b-ed9602b6bf8d2013-02-05 20:16:31.628 UTC46181b16-64e9-40aa-8dde-b32a9478fe1d2011-09-27 15:29:17.819 UTC98159653-b95c-4a97-b6b3-b400a68f0dc42013-01-29 14:17:24.662 UTCMatch concept profiles with predefined set2013-01-07 13:20:03.887 UTCea38018e-ee90-4ccb-ab8e-78eeec907cad2011-09-28 12:02:39.57 UTC0dcad6f0-b77c-4d5d-ae1b-893a7b2436a62011-09-28 12:12:42.334 UTC15145a87-30e2-4e04-97a9-10572ff64aae2011-09-28 11:37:06.330 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 UTC0e2bcc6a-21cb-4a66-a50c-42fd8b2226aa2013-01-07 13:15:58.306 UTCdacab209-3218-4181-a2f4-eaacfb1022b12013-02-04 10:17:42.374 UTC1b7115f7-7832-4081-88df-c6ce4775238f2011-09-28 11:35:31.328 UTCc55d2bf1-a3b9-46b1-a486-97b4b03eca202012-04-16 15:03:34.648 UTC60d3ffca-7a97-485f-a391-6f8273236e1c2013-02-01 11:26:19.951 UTCe48487a3-446f-42a1-9fcc-d820a9498ff02012-07-18 13:14:50.306 UTC25ac05cb-87b1-4cee-926a-4fb5c6662b8f2013-02-05 20:18:50.908 UTCdafd97bb-bd4c-4540-b335-d9cfe2d841082012-04-16 15:04:13.913 UTC526ee9ee-6592-4472-90d4-f392659ea5842013-01-29 12:44:50.692 UTCcc6b35c6-0d92-4ef7-ae5b-08eab3af670c2013-01-07 13:21:45.613 UTCae37940d-e39c-43c2-80bf-512e607102012012-04-16 12:45:48.511 UTC477ba81b-f13d-41f2-ba19-e19f6104e36e2012-09-11 12:14:41.164 UTC19844d48-41a3-49e5-8cd3-5c3ccc40ec002013-01-07 13:19:35.160 UTC494bf485-3d60-4900-88f6-060f54ef39692013-01-29 13:27:18.126 UTCde3149d9-6f9a-49cd-a542-91c18f65109d2012-09-11 12:27:01.860 UTC6036660d-2ac0-4369-a7f7-d208a0a262652012-09-11 12:31:12.75 UTC9e39fe6a-c3da-4e04-a3ee-8c8dee6aa9162013-01-28 15:31:38.841 UTCdacab209-3218-4181-a2f4-eaacfb1022b12013-02-05 11:18:43.126 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 UTC1d5bb33c-d18f-4d9c-9ead-487ab5271b7a2011-09-27 15:37:33.997 UTC680aa556-740a-433c-b63e-82a270a9d9e32013-01-29 15:48:25.704 UTC233c6660-ebf6-47c8-af02-b1884424153d2012-09-11 12:12:26.526 UTC681cb800-d7cb-4786-8c64-585df6b607c72013-02-05 19:53:51.192 UTCa78cb530-6e91-48ac-8d8b-e6bc9ce7b0fa2013-01-29 14:25:31.386 UTC91ab33da-4da0-4e22-9542-7994c993b96a2013-01-29 16:08:36.560 UTCffd57175-7b65-4edb-9086-42bad4170b462011-09-27 13:41:33.82 UTC09430282-326d-4c5b-85a8-28ddfc97753e2011-09-27 15:31:47.87 UTC3869f1dd-8db7-4881-b73a-4d55c99c60892013-02-01 15:53:09.746 UTCFilter_concepts_withConcept_ID00The input concept ID (Erasmus MC ontology format).2012-09-12 08:05:41.115 UTChttp://rdf.biosemantics.org/owl/concept#30906912013-02-05 19:59:34.930 UTCConcepts_with_profilesConcept IDs (Erasmus MC ontology format) with profiles.2012-09-12 08:06:21.459 UTChttp://rdf.biosemantics.org/owl/concept#30906912013-02-05 19:59:27.917 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/ConceptRecognizerService?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_profilesf277c166-a637-46cb-8057-994bca43747c2013-02-05 19:59:34.988 UTC2c1a5ea4-a6b9-42e4-9058-89fa645166a52013-02-05 20:30:21.742 UTC9534e0b4-b900-494d-8406-0962864ff7222013-01-28 15:05:57.217 UTCd329fbae-c150-4b5b-87d5-9ca191669ec82013-02-05 19:40:36.400 UTC23a69643-b9c9-4163-8a19-dfa1078b27132012-09-12 07:55:47.752 UTCCreator: Kristina Hettne on behalf of the BioSemantics group
Contribution: Reinout van Schouwen (Web service)2012-09-12 08:07:05.643 UTC326ad476-7c6e-435b-8003-8ba9e7ad1b122012-09-12 08:07:46.534 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 UTC88f2a1fc-f70d-4c2a-965a-20fa0b0c4d842013-02-05 11:20:15.662 UTCFilter concepts with profiles2012-09-12 08:07:23.356 UTCDatabaseID_to_ConceptIDDatabaseID00EG2012-04-24 23:16:44.86 UTCIdentifier for databases, e.g. EG for Entrez Gene
Possible values:
EG, Entrez Gene
2012-06-25 20:38:10.999 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_IDs30972122012-04-24 23:19:25.744 UTCConcept Identifiers for the given input, e.g. 3097212 for EG.30642012-04-24 23:19:16.717 UTCmapDatabaseIDToConceptIDsparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://ws.biosemantics.org/ConceptRecognizerService?wsdlmapDatabaseIDToConceptIDsnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050003net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemapDatabaseIDToConceptIDs_inputID0database0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivitydatabase0'text/plain'falseID0'text/plain'falseoutput0'text/xml'0<s:extensions 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.InvokemapDatabaseIDToConceptIDsparametersmapDatabaseIDToConceptIDs_inputIDmapDatabaseIDToConceptIDs_inputdatabasemapDatabaseIDToConceptIDs_outputinputmapDatabaseIDToConceptIDs_returninputConcept_IDsAuthors:
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 UTCc2cbb1b4-e2b2-4c45-9dfd-5323f702be832012-04-24 23:22:49.83 UTCd2f0a621-0e45-43b7-bd56-11c61a1c8df92012-07-18 13:13:11.179 UTC7ecf19fa-7ed5-489c-82e5-9b2468795c302012-09-04 11:14:44.543 UTCc690ec55-e66d-4cde-a257-f219ab1416792013-02-05 11:51:05.313 UTC60ef0156-46c6-4368-a578-e6a26823caba2013-01-28 15:03:01.417 UTC80ee33e8-dddc-4d0f-aef9-ce9790e699042012-04-24 23:12:44.984 UTC0b447fad-9299-453c-9195-e00c9fb687a72012-04-24 23:20:02.840 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 UTCcdf66f51-8d56-4a5f-87c7-5b8dbd434ee82012-07-11 14:23:57.252 UTC14fee9a1-cd21-44f2-9f28-4f2362b8d6672012-06-25 20:39:09.656 UTCDatabaseID_to_ConceptID2012-04-24 23:22:45.412 UTC