Get_HPO_concept_labebioportal_api_key00
Biportal api key to query bioportal sparql endpoint
2014-10-15 07:56:07.646 UTC
2014-10-15 12:33:10.680 UTC
file_url00
Input file url
2014-10-15 12:33:35.73 UTC
/home/rajaram/Downloads/htt-HPO-matching.xls
2014-10-15 11:47:07.676 UTC
TSV0SpreadsheetImportfileurl0D11
Extract value from column D
2014-10-15 12:34:21.10 UTC
net.sf.taverna.t2.activitiesspreadsheet-import-activity1.5net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportActivity
3
3
1
-1
true
true
true
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.InvokeGetHPOConceptInfohpoURI0bioportal_api_key0row00net.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.InvokeMerge_String_List_to_a_Stringstringlist1seperator0concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.5net.sf.taverna.t2.activities.localworker.LocalworkerActivity
stringlist
1
l('text/plain')
java.lang.String
true
seperator
0
'text/plain'
java.lang.String
true
concatenated
0
'text/plain'
0
workflow
org.embl.ebi.escience.scuflworkers.java.StringListMerge
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.Invokeseperator_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.5net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
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.InvokeSpreadsheetImportfileurlGetHPOConceptInfohpoURIGetHPOConceptInfobioportal_api_keyMerge_String_List_to_a_StringstringlistMerge_String_List_to_a_StringseperatorTSV
756b16ab-c43e-4852-a5e6-d24d8465ba3c
2014-10-14 15:34:32.646 UTC
1b4937dd-9f4f-4f15-8e2c-19af794b8be0
2014-04-17 15:59:21.62 UTC
2153da39-81d9-4251-9d62-3d8a7ef17bd9
2014-10-14 15:25:53.606 UTC
1a4b00cc-af6f-4fe0-bf39-affc19c40d89
2014-10-15 07:25:33.775 UTC
ed86431b-1856-4d13-831b-6301e24c13d9
2014-10-15 12:22:53.640 UTC
20cb2dba-9474-4789-829c-7f96a8c3b100
2014-10-14 15:35:19.367 UTC
ec310da8-8d14-4fd2-aad6-073a405442ea
2014-04-17 15:26:51.640 UTC
Rajaram kaliyaperumal, Eelke van der horst, Marco roos
2014-10-15 12:37:42.895 UTC
9d661b19-2a55-437a-b64d-60a1a2c68ef0
2014-04-16 09:07:47.745 UTC
d7f082c5-a939-4117-9559-36c721b92954
2013-06-28 05:10:23.983 UTC
fb6c57e8-0fb6-49fe-807d-19fb6fd61682
2014-04-16 09:14:49.462 UTC
2052a725-82ba-4177-bbe2-54e8cff5b45c
2014-04-16 09:12:35.268 UTC
b79dea9f-a7bb-4a42-9ebf-c8148a3baa88
2014-10-15 07:45:22.136 UTC
953358cc-aac8-4daa-a81d-4037d37f8536
2014-04-17 13:46:27.66 UTC
085064f9-fbfb-4ce9-893a-888b3fb2fa77
2014-04-16 14:15:47.970 UTC
2a420a22-54ec-4507-8a1c-ba8e4bfa9024
2014-10-15 12:17:22.319 UTC
61185ebd-5c45-463c-8d32-8c2168d0742c
2014-04-16 14:53:03.896 UTC
539f3d74-72bb-4a56-a82f-f24f0241a529
2014-04-16 09:02:36.483 UTC
a3b14355-a20c-4a35-9d1c-40d7c2442c49
2014-10-15 07:53:01.332 UTC
1c534d9c-79f2-4813-9dec-e56afc03f29b
2014-04-16 08:57:22.159 UTC
e964ef90-8c53-4416-9703-435d647b248a
2014-04-16 14:07:04.995 UTC
ceaf108f-8bc1-4fc2-b54f-2ea3629909ac
2014-10-15 11:45:10.132 UTC
e06c7ed3-519d-4f3c-a93d-848ca267a40d
2014-04-16 09:01:38.188 UTC
1e2adadb-884c-42d1-b4ca-a78f67a6e4de
2014-10-15 07:44:04.695 UTC
5c561912-d87d-4b58-9cd9-8b1e5ea3870e
2014-04-17 15:28:23.222 UTC
98dd2ae6-5e96-48dc-9b1f-47f1bbbb9390
2014-04-16 08:52:23.811 UTC
6382cf11-4c86-4022-aece-55c818a39995
2014-04-16 15:29:51.982 UTC
bf09c80d-36f8-4aa2-8f18-173043f6375b
2014-04-16 15:09:14.317 UTC
964d22a5-68e3-4101-9033-8a55de28ff9a
2014-04-16 14:57:12.764 UTC
e83ca357-6985-4221-9edf-e7fe9768ab78
2014-10-14 15:33:11.454 UTC
8ecbb29f-e0aa-47a9-8cc4-fad10dbd0a38
2014-10-15 11:46:13.615 UTC
2453b4eb-ad71-435d-9e7e-fde05f8fb29a
2014-10-20 12:30:49.679 UTC
57ac945f-fbfe-4e2a-acde-f83f4067b2d2
2014-04-16 14:38:22.770 UTC
3f48bc8d-e346-4b1b-b638-53e07ba478f4
2014-04-16 14:13:10.364 UTC
6691406d-b294-446c-95ca-137dc08c9789
2013-06-28 05:06:08.140 UTC
28012056-ffb8-43d4-a549-acb4a8d22508
2014-04-16 12:04:13.386 UTC
ef52dfc5-64b5-4839-a651-9c3ac8f3af32
2014-04-16 09:11:58.19 UTC
dbdb1aa1-b44b-4a7e-b02b-063e0ef0fc58
2014-04-16 15:18:28.24 UTC
a3dab9e6-9db0-453d-9ec6-296bd0e6b0c2
2014-04-16 09:03:15.709 UTC
87e1535f-0469-4c8f-8820-0c8c261d5a14
2014-10-15 08:01:51.380 UTC
6d8dfe81-e5af-40fc-be66-ebdec3b61436
2014-04-16 14:45:39.756 UTC
90913f2c-4e82-4586-a3c4-41aefe31a747
2014-04-16 14:41:12.46 UTC
77b5cf48-6dc1-4378-8d10-ef2d77c5d69e
2014-04-16 09:07:08.104 UTC
Get HPO concept label and synonym
2014-10-15 12:38:25.228 UTC
805ee308-a07c-4af3-87dd-8150d24abea2
2014-04-16 13:18:30.263 UTC
827e86f0-9a85-49ae-b85f-76c128ce6f4c
2014-04-16 13:17:12.946 UTC
bfe19275-b298-4a4c-8fd8-8c5603fc0b7f
2014-04-16 09:21:23.805 UTC
4b7646fc-b541-47dc-8575-a0c2bd8b4f1b
2014-04-17 13:51:36.697 UTC
bcd2067d-6455-45c8-bbf4-dfc63dc3e378
2014-04-16 09:15:41.25 UTC
4fe9896b-e25d-460c-bc97-21336ba5368d
2014-10-14 15:24:00.873 UTC
e24f901a-973e-4356-9955-261f5427539b
2014-10-15 11:47:18.775 UTC
ec503a31-578f-4f08-9ae8-72ffa80408d4
2014-04-16 15:25:27.147 UTC
277fbeb1-fee8-4850-90dc-59aa884fea37
2014-04-16 14:49:54.194 UTC
0cb3efb8-1ccb-4fc0-8c57-c59ec79ecf8b
2014-10-15 12:38:32.41 UTC
0a2ed783-c6bc-4eff-b2a9-5982b600951c
2014-04-16 14:44:19.437 UTC
0c809868-7d5f-455f-806a-61b960081a26
2014-10-15 07:32:21.147 UTC
a4b157f4-369f-4c1b-bf28-3318f916a898
2014-04-16 14:19:22.430 UTC
7f45ae50-b9cd-49a0-bb45-8f6ebe4579b8
2014-10-15 07:29:20.345 UTC
32cca822-7634-4c2e-968f-07b5ada36974
2014-04-16 11:56:21.999 UTC
a0e9e8ff-ff39-4c4b-9f8f-2a74efce6cc2
2014-10-15 07:41:45.650 UTC
357d9399-580c-4fa6-85ab-845817a5a0ba
2014-04-16 15:22:03.904 UTC
27368cc3-56b5-4fed-a32b-7ec9b87bea95
2014-10-14 15:30:26.144 UTC
941ff623-fcfb-428c-86a7-a58cbf99798f
2014-04-17 15:35:48.756 UTC
e95acc7e-8b0a-40ab-aec0-d0eafced1024
2014-10-15 07:39:28.912 UTC
Workflow1bioportal_api_key00
3a6ded3d-0768-4d32-9608-11fc205f37a2
2014-10-15 07:47:55.334 UTC
Biportal api key to query bioportal sparql endpoint
2014-10-15 07:56:07.646 UTC
hpoURI00row0REST_Service_LABELquery0apikey0responseBody00
Query biportal SAPRQL endpoint to get label for the given concept
2014-10-15 07:58:58.546 UTC
net.sf.taverna.t2.activitiesrest-activity1.5net.sf.taverna.t2.activities.rest.RESTActivity
GET
http://sparql.bioontology.org/sparql/?apikey={apikey}&query={query}
application/sparql-results+xml
application/xml
String
false
false
false
false
true
query
java.lang.String
apikey
java.lang.String
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.Invokeget_label_sparql_queryvalue00
Get concept label SPARQL query
2014-10-15 07:56:57.303 UTC
net.sf.taverna.t2.activitiesstringconstant-activity1.5net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdf: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX obo: <http://www.geneontology.org/formats/oboInOWL#>
SELECT DISTINCT ?label {
?concept rdfs:label ?label.
}
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.Invokebind_urigetLabel0getSynonym0hpoURI0sparlGetLabel00sparqlGetSynonym00
Bind HPO URI to the sparql query and remove blank lines
2014-10-15 07:55:30.877 UTC
net.sf.taverna.t2.activitiesbeanshell-activity1.5net.sf.taverna.t2.activities.beanshell.BeanshellActivity
getLabel
0
text/plain
java.lang.String
true
hpoURI
0
text/plain
java.lang.String
true
getSynonym
0
text/plain
java.lang.String
true
sparlGetLabel
0
0
sparqlGetSynonym
0
0
workflow
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.Invokelabelxml_text0nodelist11
Extract label from the xml reponse
2014-10-15 08:00:22.52 UTC
net.sf.taverna.t2.activitiesxpath-activity1.5net.sf.taverna.t2.activities.xpath.XPathActivity
<?xml version="1.0" encoding="UTF-8"?>
<sparql xmlns="http://www.w3.org/2005/sparql-results#">
<head>
<variable name="label"/>
</head>
<results>
<result>
<binding name="label"><literal datatype="http://www.w3.org/2001/XMLSchema#string">Amyotrophic lateral sclerosis</literal></binding>
</result>
</results>
</sparql>
/default:sparql/default:results/default:result/default:binding/default:literal
default
http://www.w3.org/2005/sparql-results#
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.Invokeget_synonym_sparql_queryvalue00
Get concept synonym SPARQL query
2014-10-15 07:57:16.200 UTC
net.sf.taverna.t2.activitiesstringconstant-activity1.5net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdf: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX obo: <http://www.geneontology.org/formats/oboInOWL#>
SELECT DISTINCT ?synonym {
?concept obo:hasExactSynonym ?synonym.
}
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.InvokeREST_Service_SYNONYMquery0apikey0responseBody00
Query biportal SAPRQL endpoint to get synonyms for the given concept
2014-10-15 07:59:33.916 UTC
net.sf.taverna.t2.activitiesrest-activity1.5net.sf.taverna.t2.activities.rest.RESTActivity
GET
http://sparql.bioontology.org/sparql/?apikey={apikey}&query={query}
application/sparql-results+xml
application/xml
String
false
false
false
false
true
query
java.lang.String
apikey
java.lang.String
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.Invokesynonymxml_text0nodelist11
Extract synonym from the xml reponse
2014-10-15 08:00:41.181 UTC
net.sf.taverna.t2.activitiesxpath-activity1.5net.sf.taverna.t2.activities.xpath.XPathActivity
<?xml version="1.0" encoding="UTF-8"?>
<sparql xmlns="http://www.w3.org/2005/sparql-results#">
<head>
<variable name="synonym"/>
</head>
<results>
<result>
<binding name="synonym"><literal datatype="http://www.w3.org/2001/XMLSchema#string">Choreic movements</literal></binding>
</result>
<result>
<binding name="synonym"><literal datatype="http://www.w3.org/2001/XMLSchema#string">Choreiform movements</literal></binding>
</result>
</results>
</sparql>
/default:sparql/default:results/default:result/default:binding/default:literal
default
http://www.w3.org/2005/sparql-results#
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.InvokeFlatten_List_2inputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.5net.sf.taverna.t2.activities.localworker.LocalworkerActivity
inputlist
2
l(l(''))
[B
true
outputlist
1
l('')
1
workflow
org.embl.ebi.escience.scuflworkers.java.FlattenList
net.sf.taverna.t2.coreworkflowmodel-impl1.5net.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.InvokeMerge_String_List_to_a_Stringstringlist1seperator0concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.5net.sf.taverna.t2.activities.localworker.LocalworkerActivity
stringlist
1
l('text/plain')
java.lang.String
true
seperator
0
'text/plain'
java.lang.String
true
concatenated
0
'text/plain'
0
workflow
org.embl.ebi.escience.scuflworkers.java.StringListMerge
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
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