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>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-impl1.5net.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>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-impl1.5net.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>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-impl1.5net.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_inputIDmapDatabaseIDToConceptIDs_inputdatabaseHPO_UMLS_mappingumls_hpo_mapping_file_urlmapDatabaseIDToConceptIDs_outputinputmapDatabaseIDToConceptIDs_returninputHPO_IDUMLS_IDConceptID
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_sheetfileurlhpo_listumls_list
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