Get_a_list_of_proteins_annotated_with_an_Ontology_term_and_use_these_proteins_to_query_BioModelsTaxonomyId0096062012-02-20 23:50:41.514 UTCTaxonomy ID used to describe Species. Search for a taxonomy ID in "www.uniprot.org/browse/taxonomy". Set a value with empty content to search for all the species.2012-02-20 23:51:06.488 UTCGeneOntologyId00Gene Ontology Id2012-02-20 23:58:55.0 UTCGO:00480692012-08-24 02:37:44.962 UTCproteinListFromGOBioModelsIdsSBMLBioModelsUrlGet_a_list_of_proteins_from_a_Gene_Ontology__GO__termTaxonomyId0GeneOntologyId0listOfProteins00net.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.InvokeParse_QuickGO__proteinList__file_formatquickGoProteinListFormat0header0idList11net.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.Invokeheader_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivitytruenet.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_models_from_BioMUniProtId0BioModelsIds11SBML11BioModelsUrl11net.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_a_list_of_proteins_from_a_Gene_Ontology__GO__termTaxonomyIdGet_a_list_of_proteins_from_a_Gene_Ontology__GO__termGeneOntologyIdParse_QuickGO__proteinList__file_formatquickGoProteinListFormatParse_QuickGO__proteinList__file_formatheaderGet_models_from_BioMUniProtIdproteinListFromGOBioModelsIdsSBMLBioModelsUrl37ee5e94-436a-4753-8a2c-e38ed4ad1a372012-08-24 02:42:59.237 UTC4d82c528-3729-4b16-bc0f-a204c5dfce322012-08-24 02:33:42.687 UTC92690bf7-6ee7-49f2-9acc-600eb711672e2012-08-22 08:03:53.493 UTC736ee129-7e17-42ce-9526-d980437906082012-02-22 21:10:15.187 UTCRafael C. Jimenez2012-02-20 23:51:28.938 UTCGet a list of proteins annotated with an Ontology term and use these proteins to query BioModels2012-08-22 08:02:16.264 UTCd0304540-79d7-4a41-ba31-ba352911880d2012-02-22 21:14:44.544 UTC9b435316-0d01-46ce-b9ad-6146c2f70cea2012-02-20 23:59:03.336 UTC7f631a30-b1f0-485c-a34c-82b7363e3a722012-08-22 07:57:24.77 UTCA service to look for models in BioModels using an Ontology Id as input. First the workflow will look in QuickGO for UniProt accessions annotated with the provided Ontology Id. Then it will look for models using the list of proteins. If one of the input protein is found in one model the workflow will provide the BioModels Id, the SBML and a link to the BioModels database. Please use taverna 2.4 or above.2012-08-24 02:42:49.186 UTCParse_QuickGO__proteinList__file_formatquickGoProteinListFormat00DB ID Symbol Name Synonym Type Taxon
UniProtKB C9JJU6 SUN1 Sad1 and UNC84 domain containing 1 C9JJU6_HUMAN|SUN1|IPI00894185 protein 9606
UniProtKB C9JK55 SUN1 Sad1 and UNC84 domain containing 1 C9JK55_HUMAN|SUN1|IPI00955411 protein 9606
UniProtKB C9JKI3 CAV1 Caveolin C9JKI3_HUMAN|CAV1|IPI00852906 protein 9606
UniProtKB C9JR15 SUN1 Sad1 and UNC84 domain containing 1 C9JR15_HUMAN|SUN1|IPI00894370 protein 9606
2012-02-20 23:14:30.760 UTCList of proteins in the QuickGO "proteinList" format. Check "Download formats" for more inforamtion in "http://www.ebi.ac.uk/QuickGO/reference.html"2012-02-20 23:12:56.988 UTCheader00true2012-02-20 23:18:02.771 UTCDoes the file include the header?2012-02-20 23:18:14.505 UTCnameListidListsynonymListtaxonListtypeListsymbolListprocessQuickGoProteinListFormatquickGoProteinListFormat0header0idList11synonymList11taxonList11typeList11nameList11symbolList11net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivityquickGoProteinListFormat0text/plainjava.lang.Stringtrueheader0text/plainjava.lang.StringtrueidList11synonymList11typeList11taxonList11nameList11symbolList11dbList11workflownet.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.InvokeprocessQuickGoProteinListFormatquickGoProteinListFormatprocessQuickGoProteinListFormatheadernameListidListsynonymListtaxonListtypeListsymbolList699f4e8b-7b76-4825-8e7c-21ee30e6ace42012-02-20 22:50:17.105 UTC65261095-88ff-4057-8810-86719e362b222012-02-20 22:46:32.146 UTCaf4188d2-aacb-4345-987a-2904ccb6d9212012-02-20 22:27:47.278 UTC7cffdca6-4e7e-460b-96b5-15d6ef53157b2012-02-20 22:44:58.789 UTC5bd1e0e9-30b9-4c72-a097-fbd2880221be2012-02-20 21:35:41.916 UTCParse QuickGO "proteinList" file format. http://www.ebi.ac.uk/QuickGO/reference.html2012-02-20 23:21:14.686 UTC21c64d91-08ab-4583-8f96-6923b50211c42012-02-20 23:21:17.70 UTCParse QuickGO "proteinList" file format2012-02-20 23:09:54.660 UTCRafael C. Jimenez2012-02-20 21:22:11.198 UTC65c514d6-d7b1-44be-af29-1f5ec76173c52012-02-19 22:50:36.671 UTCf09568c5-4617-4ad1-a7da-eab0e4f3350d2012-02-20 22:40:50.956 UTC4d990e35-5f26-4c98-bb20-8db5744999712012-02-20 21:24:11.725 UTCf699f0af-1e29-4419-bdd8-85281cf001f02012-02-20 23:20:10.758 UTC24fde965-3770-4c10-a0f4-919ba249f52d2012-02-20 23:14:10.417 UTC9d81aafa-f875-419a-89f1-781ff803c7ef2012-02-20 22:35:55.748 UTCee83b6ea-549c-4ada-8fd6-8eec8e801cc52012-02-20 21:21:53.494 UTC5f7bfa79-4c99-4593-a244-003f7a2541a52012-02-20 22:51:22.41 UTCbd2f222c-3793-47f4-9c7c-0b87d37f06132012-02-20 22:52:09.878 UTCGet_models_from_BioMUniProtId00UniProt accession2012-08-22 05:09:54.853 UTCP371732012-08-22 05:10:00.308 UTCBioModelsIdsBIOMD0000000163
BIOMD0000000101
BIOMD0000000342
BIOMD0000000173
BIOMD00000001122012-08-22 05:11:15.14 UTCList of model identifiers from BioModels2012-08-22 05:11:36.115 UTCSBMLBioModelsUrlgetModelsIdByUniprotIduniprotId0getModelsIdByUniprotIdReturn11net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://www.ebi.ac.uk/biomodels-main/services/BioModelsWebServices?wsdlgetModelsIdByUniprotIdnet.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.InvokegetModelSBMLByIdid0getModelSBMLByIdReturn00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://www.ebi.ac.uk/biomodels-main/services/BioModelsWebServices?wsdlgetModelSBMLByIdnet.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.InvokeGetBiomodelsUrlBiomodelsId0BiomodelsUrl00net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivityBiomodelsId0text/plainjava.lang.StringtrueBiomodelsUrl00workflownet.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.InvokegetModelsIdByUniprotIduniprotIdgetModelSBMLByIdidGetBiomodelsUrlBiomodelsIdBioModelsIdsSBMLBioModelsUrlefd8b80d-407a-4149-9826-93172f276f802012-08-24 02:17:34.386 UTCA service to look for models in BioModels using a UniProt accession as input. If the input protein is found in one model the workflow will provide the BioModels Id, the SBML and a link to the BioModels database. Please use taverna 2.4 or above.2012-08-24 02:29:58.523 UTCc128c3c6-e35f-458c-8d79-aba048e6ec5a2012-08-22 03:20:53.662 UTCf76fc0cc-05ae-4114-a07b-daf670d2cc342012-08-24 02:26:34.534 UTC1634845c-4841-4b18-bd8a-649af1cc4ed32012-08-24 02:24:51.27 UTCa969986e-0f03-4619-af18-aab3b56397bd2012-08-24 02:30:01.105 UTC46f50814-730e-4ef4-87fd-d45f6798f0a32012-08-22 03:17:57.311 UTCRafael C. Jimenez2012-08-24 02:24:53.290 UTCGet models from BioModels including the input protein.2012-08-24 02:24:45.720 UTC487bd2d0-47a8-491b-ad50-c3f900de45fc2012-08-22 06:03:15.88 UTCGet_a_list_of_proteins_from_a_Gene_Ontology__GO__termGeneOntologyId00GO:00020802012-02-19 22:39:10.360 UTCGene Ontology Id2012-02-19 22:38:58.104 UTCTaxonomyId00Taxonomy ID used to describe Species. Search for a taxonomy ID in "www.uniprot.org/browse/taxonomy". Set a value with empty content to search for all the species.2012-02-20 21:21:43.84 UTC96062012-02-19 22:39:24.72 UTCstatus2002012-02-19 22:49:52.211 UTCHTTP response status codes. http://en.wikipedia.org/wiki/List_of_HTTP_status_codes2012-02-19 22:49:29.724 UTClistOfProteinsDB ID Symbol Name Synonym Type Taxon
UniProtKB Q9QUK6 Tlr4 Toll-like receptor 4 TLR4_MOUSE|Tlr4|Lps|IPI00131730|Q9D691|Q9QZF5|Q9Z203 protein 10090
2012-02-19 22:44:15.832 UTCResults in Tab Separated Values (TSV)2012-02-19 22:44:03.860 UTCQuickGODatabase0Format0GoId0TaxId0status00responseBody00net.sf.taverna.t2.activitiesrest-activity1.4net.sf.taverna.t2.activities.rest.RESTActivityGEThttp://www.ebi.ac.uk/QuickGO/GAnnotation?goid={GoId}&db={Database}&format={Format}&tax={TaxId}text/tab-separated-valuesapplication/xmlStringfalsefalsefalsefalsefalseFormatjava.lang.StringDatabasejava.lang.StringTaxIdjava.lang.StringGoIdjava.lang.Stringnet.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.InvokeDatabasevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivityUniProtKBnet.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.InvokeFormatvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivityproteinListnet.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.InvokeQuickGODatabaseQuickGOFormatQuickGOGoIdQuickGOTaxIdstatuslistOfProteins214af3fd-850d-467e-992a-4de0cb2670d32012-02-20 22:57:08.806 UTC5bd1e0e9-30b9-4c72-a097-fbd2880221be2012-02-20 21:35:41.916 UTC4d990e35-5f26-4c98-bb20-8db5744999712012-02-20 21:24:11.725 UTC65c514d6-d7b1-44be-af29-1f5ec76173c52012-02-19 22:50:36.671 UTCGet a list of proteins from a Gene Ontology (GO) term2012-02-20 21:23:15.307 UTCee83b6ea-549c-4ada-8fd6-8eec8e801cc52012-02-20 21:21:53.494 UTCf70cfe42-70e5-44b8-a9e5-8e5a9add97792012-02-20 22:59:15.786 UTCGet a list of UniProt proteins that have been annotated with the same Gene Ontology (GO) term. This workflow use the the QuicGO service2012-02-20 22:59:11.564 UTCRafael C. Jimenez2012-02-20 21:22:11.198 UTC