HPO_UMLS_ConceptID_mumls_hpo_mapping_file_url00 /home/marco/Work/HandsOn/Workflows/BioSemantics/CPAWorkflows/sources/hpo_umls-2013AB-20140418-test.xls 2014-10-11 23:28:48.52 UTC Excel sheet containing the UMLS-HPO mappings. Columns: <HPO-ID>|<UMLS-ID> E.g. HP_0000001|C0023449 HP_0000001|C1961102 HP_0000003|C0345335 Examples: W:\HandsOn\Workflows\BioSemantics\CPA Workflows\sources\hpo_umls-2013AB-20140418-test.xls /home/marco/Work/HandsOn/Workflows/BioSemantics/CPAWorkflows/sources/hpo_umls-2013AB-20140418-test.xls 2014-10-11 23:29:00.939 UTC HPO_ID1UMLS_ID1ConceptID1mapDatabaseIDToConceptIDsparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.5net.sf.taverna.t2.activities.wsdl.WSDLActivity http://ws.biosemantics.org/ConceptProfileMiningService?wsdl mapDatabaseIDToConceptIDs net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemapDatabaseIDToConceptIDs_inputID0database0output00net.sf.taverna.t2.activitieswsdl-activity1.5net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity database 0 'text/plain' false ID 0 'text/plain' false output 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="mapDatabaseIDToConceptIDs" name="parameters" qname="{http://services.conceptprofilemining.lumc.nl/}mapDatabaseIDToConceptIDs"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="database" qname="mapDatabaseIDToConceptIDs&gt;database" /><s:basetype optional="true" unbounded="false" typename="string" name="ID" qname="mapDatabaseIDToConceptIDs&gt;ID" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeHPO_UMLS_mappingumls_hpo_mapping_file_url0hpo_list11umls_list11 Workflow to extract HPO-UMLS mapping in two lists 2014-10-11 22:27:47.160 UTC net.sf.taverna.t2.activitiesdataflow-activity1.5net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokedatabase_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.5net.sf.taverna.t2.activities.stringconstant.StringConstantActivity umls net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemapDatabaseIDToConceptIDs_outputinput0return00net.sf.taverna.t2.activitieswsdl-activity1.5net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false return 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="mapDatabaseIDToConceptIDsResponse" name="parameters" qname="{http://services.conceptprofilemining.lumc.nl/}mapDatabaseIDToConceptIDsResponse"><s:elements><s:complextype optional="true" unbounded="false" typename="conceptSetWrapper" name="return" qname="mapDatabaseIDToConceptIDsResponse&gt;return"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptIDsAsString" qname="conceptSetWrapper&gt;conceptIDsAsString" /></s:elements></s:complextype></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemapDatabaseIDToConceptIDs_returninput0conceptIDsAsString00net.sf.taverna.t2.activitieswsdl-activity1.5net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false conceptIDsAsString 0 'text/plain' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="true" unbounded="false" typename="conceptSetWrapper" name="return" qname="mapDatabaseIDToConceptIDsResponse&gt;return"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="conceptIDsAsString" qname="conceptSetWrapper&gt;conceptIDsAsString" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemapDatabaseIDToConceptIDsparametersmapDatabaseIDToConceptIDs_inputoutputmapDatabaseIDToConceptIDs_inputIDHPO_UMLS_mappingumls_listmapDatabaseIDToConceptIDs_inputdatabasedatabase_valuevalueHPO_UMLS_mappingumls_hpo_mapping_file_urlumls_hpo_mapping_file_urlmapDatabaseIDToConceptIDs_outputinputmapDatabaseIDToConceptIDsparametersmapDatabaseIDToConceptIDs_returninputmapDatabaseIDToConceptIDs_outputreturnHPO_IDHPO_UMLS_mappinghpo_listUMLS_IDHPO_UMLS_mappingumls_listConceptIDmapDatabaseIDToConceptIDs_returnconceptIDsAsString HPO-UMLS-ConceptID mapping 2014-10-11 23:32:47.15 UTC ef4f3bfe-8cff-4225-8869-b6bdb03519b6 2014-10-10 09:54:43.604 UTC 11038ed3-2b3c-4951-9953-3d5aa2e7c169 2014-10-10 13:56:10.117 UTC 91def53e-41a5-49e3-9874-4f649d68c0f0 2014-09-19 07:48:02.89 UTC Marco Roos on behalf of the BioSemantics group LUMC 2014-10-11 23:32:21.994 UTC 5fee839c-c147-496d-88a0-a37f1b2b8dca 2014-10-11 22:25:40.693 UTC 3f2bf60e-0278-4b57-a2b4-d6e9f814f633 2014-10-11 23:29:07.316 UTC 4a2ddc84-d065-4c4a-9e83-a52d6058d65f 2014-10-10 09:53:33.567 UTC 46745a1b-b464-4877-bfc1-d85fa0948a82 2014-10-11 23:31:59.776 UTC 7ab59681-5945-471c-950a-37f810df807e 2014-10-11 23:10:00.53 UTC 042d765a-26e1-43bb-b541-90f0e6b4bd0e 2014-10-10 09:57:22.441 UTC 14d91579-ad56-4dd7-9a0b-661b067c5a5c 2014-10-11 23:26:55.249 UTC 420687d6-69b3-4c74-bcef-f5f30cc99387 2014-10-11 23:34:47.715 UTC Generate HPO-Concept profiles via HPO-UMLS mappings. The result is a list of Concept IDs corresponding to Concept profiles for UMLS concepts that approximate HPO concepts. The output is a table of UMLS-ID, HPO- ID, COncept-ID rows. 2014-10-11 23:34:41.377 UTC 3137caff-f029-49e7-920d-da8e6d7d7f97 2014-10-11 22:28:07.665 UTC Workflow1umls_hpo_mapping_file_url00 Excel sheet containing the UMLS-HPO mappings. <HPO-ID>|<UMLS-ID> E.g. HP_0000001|C0023449 HP_0000001|C1961102 HP_0000003|C0345335 2014-10-11 23:09:02.259 UTC /home/marco/Work/HandsOn/Workflows/BioSemantics/CPAWorkflows/sources/hpo_umls-2013AB-20140418-test.xls 2014-10-11 23:18:33.997 UTC hpo_list1umls_list1Import_UMLS_HPO_sheetfileurl0HPO11UMLS11net.sf.taverna.t2.activitiesspreadsheet-import-activity1.5net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportActivity 0 1 0 -1 A HPO B UMLS true false false EMPTY_STRING PORT_PER_COLUMN , net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeImport_UMLS_HPO_sheetfileurlumls_hpo_mapping_file_urlhpo_listImport_UMLS_HPO_sheetHPOumls_listImport_UMLS_HPO_sheetUMLS 8ce30777-7090-46e9-85ba-9597aff1f642 2014-10-11 23:13:21.409 UTC ef4f3bfe-8cff-4225-8869-b6bdb03519b6 2014-10-10 09:54:43.604 UTC 91def53e-41a5-49e3-9874-4f649d68c0f0 2014-09-19 07:48:02.89 UTC 4a2ddc84-d065-4c4a-9e83-a52d6058d65f 2014-10-10 09:53:33.567 UTC 1f2566df-6c03-4362-8d94-9cb49010e003 2014-10-10 10:15:43.334 UTC 3bc8c020-2458-4599-8efb-28cd156fdcf0 2014-10-10 13:35:09.236 UTC 2e50e0ee-6d87-4b49-85cc-19bb1041c836 2014-10-10 09:55:56.992 UTC 204170c2-7581-4eee-9f2f-adae0d9393c5 2014-10-10 13:12:34.835 UTC e5ea5fb0-a16a-41fe-a30f-8ab423770156 2014-10-10 10:15:05.265 UTC 7dc74139-bcec-42bc-8d41-fa30f52173e1 2014-10-10 10:05:15.873 UTC 3850b83f-ec17-42ec-ba04-d51028f9ad9f 2014-10-10 10:07:15.100 UTC e5342cc4-6044-4537-bdaa-e2da42fa0963 2014-10-10 13:21:41.38 UTC 97a0c4aa-8519-4905-95f7-f1b32333ec74 2014-10-10 13:33:14.153 UTC 7bc72cc7-da5e-454c-bc52-590b448050b8 2014-10-11 23:11:43.612 UTC f1f7721d-7994-4856-8890-ac273a5dc00d 2014-10-11 22:25:02.129 UTC becc4e2d-b95b-4b05-98b1-6fcaf6f5c896 2014-10-10 09:56:48.137 UTC 861b5bbf-81ea-4adb-b0b7-2336f0be507f 2014-10-10 10:17:21.843 UTC 2cbbbda1-32b9-4dcc-9c8d-aa1459f1e91a 2014-10-10 13:17:10.492 UTC 0185849f-5b5c-4140-a4d2-7bf496badbd4 2014-10-11 23:05:46.82 UTC b0f70ad3-0429-4600-9277-59ab1890f3f3 2014-10-11 23:17:13.267 UTC 0a39a911-0f14-4aee-9bfb-225ef0627167 2014-10-10 10:14:05.702 UTC c6304952-6251-4b35-90ae-73a642785980 2014-10-10 13:39:20.41 UTC 499fc2b9-99e9-4c6c-9006-255bb4b5d983 2014-10-11 23:18:37.382 UTC 7481ab28-870f-4d95-a11c-99837dbc09b8 2014-10-11 23:09:04.779 UTC 79add1d8-7d3b-4c6c-a985-196e71413388 2014-10-10 10:06:12.923 UTC e0d1a962-d0e3-4c23-8bd5-2ff82f918eef 2014-10-11 23:10:21.96 UTC