DAS_features_retrieval_and_parsing_with_JDASIDs00You can input more than one ID using comma-separated values. You can use different types of IDs depending on the DAS coordinate system (http://www.dasregistry.org/help_coordsys.jsp) you decided to use. If you selected a DAS source of type "Protein Sequence" and authority "UniProt" you could use UniProt (TrEMBL and SwissProt) accessions. For instance "P37173". If you selected a DAS source of type "Chromosome", authority "GRCh_37" and organism "Homo sapiens" you could use a chromosome ID. For instance "1".2011-06-01 18:02:00.987 BSTO35502,P999992011-06-01 17:52:23.956 BSTDasSource00Input a DAS reference source following this format "http://www.server.com/das/source/". Find a public list of available DAS reference sources providing sequence information in the DAS registry … http://www.dasregistry.org/listSources.jsp … or create your own DAS source with easyDAS … http://www.ebi.ac.uk/panda-srv/easydas/2011-06-01 18:02:13.393 BSThttp://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/2011-06-01 17:52:09.237 BSTstart00The start and stop attributes indicate the range of the segment to query. In this workflow is optional. Set an empty value to get the whole sequence.2011-06-01 18:02:23.330 BSTstop00The start and stop attributes indicate the range of the segment to query. In this workflow is optional. Set an empty value to get the whole sequence.2011-06-01 18:02:48.751 BSTFeatures_DAS_formatHave a look to the specification to know more about the DAS format ... http://www.biodas.org/documents/spec-1.6.html#features2011-06-01 18:03:25.265 BSTService_statusHTTP response status codes ... http://en.wikipedia.org/wiki/List_of_HTTP_status_codes 2011-06-01 18:03:36.624 BST2002011-06-01 18:03:43.327 BSTFeatures_custom_formatThis output was achieved using the JDAS library …
http://code.google.com/p/jdas/
To be able to use this workflow with JDAS copy this file …
http://www.ebi.ac.uk/~maven/m2repo/uk/ac/ebi/das/jdas/1.0.3/jdas-1.0.3.jar
… to the lib folder inside the Taverna application. This jar file is a dependency needed to parse DAS outputs.2011-06-01 18:03:04.407 BSTDAS_features_retrievalID0DasSource0start0stop0Features_DAS_format00Service_status00net.sf.taverna.t2.activitiesdataflow-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesplit_by_regexregex0string0split11net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivitystring0'text/plain'java.lang.Stringtrueregex0'text/plain'java.lang.Stringtruesplit11workfloworg.embl.ebi.escience.scuflworkers.java.SplitByRegexUserNameHere2011-05-30 02:58:05.622 BSTnet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregex_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity,net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeJDASfeaturesXML0featuresText00net.sf.taverna.t2.activitiesbeanshell-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivityfeaturesXML0text/plainjava.lang.StringtruefeaturesText00workflownet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeDAS_features_retrievalIDDAS_features_retrievalDasSourceDAS_features_retrievalstartDAS_features_retrievalstopsplit_by_regexregexsplit_by_regexstringJDASfeaturesXMLFeatures_DAS_formatService_statusFeatures_custom_formatb976dd39-e516-4822-8659-da1deb0fb8aa2011-06-01 18:00:01.554 BSTb681062d-ff02-4b1b-b4fa-2f66180715dc2011-06-01 18:03:44.296 BST8068892f-36ca-4115-a21c-fed00b6fa9d22011-06-01 18:05:41.245 BST064f4ec4-f0ad-4c1b-a8ce-9a87015f96e62011-06-01 17:59:13.259 BSTRetrieve Protein or Genome features using the Distributed Annotation System (DAS) and create your own text output by modifying the JDAS component. To be able to use this workflow with JDAS copy this file …
http://www.ebi.ac.uk/~maven/m2repo/uk/ac/ebi/das/jdas/1.0.3/jdas-1.0.3.jar
… to the lib folder inside the Taverna application. This jar file is a dependency needed to parse DAS outputs.2011-06-01 18:05:40.41 BST480db7ab-dd76-41f5-807e-b29e2e1be8c02011-06-01 17:53:06.471 BSTDAS features retrieval and parsing with JDAS2011-06-01 18:05:07.730 BSTa024e92e-5283-4f74-86ba-005cbef495f62011-06-01 17:21:28.994 BSTDAS_features_retrievalID00You can use different types of IDs depending on the DAS coordinate system (http://www.dasregistry.org/help_coordsys.jsp) you decided to use. If you selected a DAS source of type "Protein Sequence" and authority "UniProt" you could use UniProt (TrEMBL and SwissProt) accessions. For instance "P37173". If you selected a DAS source of type "Chromosome", authority "GRCh_37" and organism "Homo sapiens" you could use a chromosome ID. For instance "1".2011-05-30 00:52:17.550 BSTP371732011-05-30 00:52:18.805 BSTDasSource00Input a DAS annotation source following this format "http://www.server.com/das/source/". Find a public list of available DAS annotation sources providing sequence information in the DAS registry … http://www.dasregistry.org/listSources.jsp … or create your own DAS source with easyDAS … http://www.ebi.ac.uk/panda-srv/easydas/2011-06-01 17:06:39.442 BSThttp://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/2011-05-30 00:28:16.88 BSTstart00The start and stop attributes indicate the range of the segment to query. In this workflow is optional. Set an empty value to get the whole sequence.2011-05-30 01:17:50.251 BST112011-05-30 00:55:19.329 BSTstop00The start and stop attributes indicate the range of the segment to query. In this workflow is optional. Set an empty value to get the whole sequence.2011-05-30 01:18:12.559 BST342011-05-30 00:55:40.282 BSTFeatures_DAS_formatHave a look to the specification to know more about the DAS format ... http://www.biodas.org/documents/spec-1.6.html#features2011-06-01 17:08:05.240 BSTService_statusHTTP response status codes ... http://en.wikipedia.org/wiki/List_of_HTTP_status_codes 2011-05-30 01:22:21.891 BST2002011-05-30 01:22:25.299 BSTGet_FeaturesID0range0DasSource0responseBody00status00net.sf.taverna.t2.activitiesrest-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.rest.RESTActivityGET{DasSource}features?segment={ID}{range}text/plainapplication/xmlStringfalsefalsefalserangejava.lang.StringIDjava.lang.StringDasSourcejava.lang.Stringnet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokecreate_rangestart0stop0range00net.sf.taverna.t2.activitiesbeanshell-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivitystart0text/plainjava.lang.Stringtruestop0text/plainjava.lang.Stringtruerange00workflownet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGet_FeaturesIDGet_FeaturesrangeGet_FeaturesDasSourcecreate_rangestartcreate_rangestopFeatures_DAS_formatService_status1666f142-70c6-49a3-b19b-c833bc6a22a82011-05-30 01:01:31.744 BST92ff601d-9ad6-4731-b9a7-6e3d292b2be72011-05-30 00:57:19.424 BST730c1649-36b7-4a8f-9243-1bc86b91803a2011-05-30 01:06:27.364 BSTa8bada53-c671-4e50-ade0-8e34c32901e62011-05-30 01:18:01.306 BST2b8cbaeb-375e-40c9-ad77-7e4ab49c057f2011-05-30 01:03:47.677 BSTedf775f1-683a-4fbe-a7c2-dfa731ca84b52011-05-30 00:34:56.825 BST93e3904a-0744-418f-a528-a56516e0c7462011-05-30 00:59:54.881 BSTRetrieve Protein or Genome features (annotations) using the Distributed Annotation System (DAS).2011-06-01 17:05:03.417 BSTRafael C. Jimenez2011-05-30 00:51:35.732 BST0211c48c-94f4-460c-a68a-999184c28c0b2011-06-01 17:08:23.88 BST79201635-7ebc-4498-aa96-286c5e6279b42011-05-30 01:16:24.682 BSTfc528ec7-bb47-49dc-81ee-c39d697fff3d2011-05-30 01:11:31.834 BST5ac5004d-9ed3-4196-9388-c6a66dfe1ad62011-05-30 01:09:39.158 BST733432d7-c241-4e41-a456-7a66a34d8d9b2011-05-30 00:58:53.465 BST9644404d-5f8d-492a-b3d8-c745997f3aa02011-05-30 01:13:55.383 BSTDAS features retrieval2011-06-01 17:05:16.463 BSTb1b262e0-bddb-47d9-80f8-507b989561132011-05-30 01:08:08.718 BST5ca5196d-90d7-458c-8c9a-f5baee1bc0d92011-06-01 17:03:02.20 BST2602b9f0-2792-4dff-9128-09ced44868192011-06-01 17:59:03.41 BST73bbadd7-3fb6-4f7c-abe3-3da636e96b342011-05-30 01:23:53.286 BST