Get_a_list_of_proteins_annotated_with_an_Ontology_term_and_use_these_proteins_to_query_BioModelsTaxonomyId00 9606 2012-02-20 23:50:41.514 UTC Taxonomy 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 UTC GeneOntologyId00 Gene Ontology Id 2012-02-20 23:58:55.0 UTC GO:0048069 2012-08-24 02:37:44.962 UTC proteinListFromGOBioModelsIdsSBMLBioModelsUrlGet_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.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.StringConstantActivity true net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGet_a_list_of_proteins_from_a_Gene_Ontology__GO__termTaxonomyIdTaxonomyIdGet_a_list_of_proteins_from_a_Gene_Ontology__GO__termGeneOntologyIdGeneOntologyIdParse_QuickGO__proteinList__file_formatquickGoProteinListFormatGet_a_list_of_proteins_from_a_Gene_Ontology__GO__termlistOfProteinsParse_QuickGO__proteinList__file_formatheaderheader_valuevalueGet_models_from_BioMUniProtIdParse_QuickGO__proteinList__file_formatidListproteinListFromGOParse_QuickGO__proteinList__file_formatidListBioModelsIdsGet_models_from_BioMBioModelsIdsSBMLGet_models_from_BioMSBMLBioModelsUrlGet_models_from_BioMBioModelsUrl 37ee5e94-436a-4753-8a2c-e38ed4ad1a37 2012-08-24 02:42:59.237 UTC 4d82c528-3729-4b16-bc0f-a204c5dfce32 2012-08-24 02:33:42.687 UTC 92690bf7-6ee7-49f2-9acc-600eb711672e 2012-08-22 08:03:53.493 UTC 736ee129-7e17-42ce-9526-d98043790608 2012-02-22 21:10:15.187 UTC Rafael C. Jimenez 2012-02-20 23:51:28.938 UTC Get a list of proteins annotated with an Ontology term and use these proteins to query BioModels 2012-08-22 08:02:16.264 UTC d0304540-79d7-4a41-ba31-ba352911880d 2012-02-22 21:14:44.544 UTC 9b435316-0d01-46ce-b9ad-6146c2f70cea 2012-02-20 23:59:03.336 UTC 7f631a30-b1f0-485c-a34c-82b7363e3a72 2012-08-22 07:57:24.77 UTC A 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 UTC Parse_QuickGO__proteinList__file_formatquickGoProteinListFormat00 DB 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 UTC List 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 UTC header00 true 2012-02-20 23:18:02.771 UTC Does the file include the header? 2012-02-20 23:18:14.505 UTC nameListidListsynonymListtaxonListtypeListsymbolListprocessQuickGoProteinListFormatquickGoProteinListFormat0header0idList11synonymList11taxonList11typeList11nameList11symbolList11net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity quickGoProteinListFormat 0 text/plain java.lang.String true header 0 text/plain java.lang.String true idList 1 1 synonymList 1 1 typeList 1 1 taxonList 1 1 nameList 1 1 symbolList 1 1 dbList 1 1 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeprocessQuickGoProteinListFormatquickGoProteinListFormatquickGoProteinListFormatprocessQuickGoProteinListFormatheaderheadernameListprocessQuickGoProteinListFormatnameListidListprocessQuickGoProteinListFormatidListsynonymListprocessQuickGoProteinListFormatsynonymListtaxonListprocessQuickGoProteinListFormattaxonListtypeListprocessQuickGoProteinListFormattypeListsymbolListprocessQuickGoProteinListFormatsymbolList 699f4e8b-7b76-4825-8e7c-21ee30e6ace4 2012-02-20 22:50:17.105 UTC 65261095-88ff-4057-8810-86719e362b22 2012-02-20 22:46:32.146 UTC af4188d2-aacb-4345-987a-2904ccb6d921 2012-02-20 22:27:47.278 UTC 7cffdca6-4e7e-460b-96b5-15d6ef53157b 2012-02-20 22:44:58.789 UTC 5bd1e0e9-30b9-4c72-a097-fbd2880221be 2012-02-20 21:35:41.916 UTC Parse QuickGO "proteinList" file format. http://www.ebi.ac.uk/QuickGO/reference.html 2012-02-20 23:21:14.686 UTC 21c64d91-08ab-4583-8f96-6923b50211c4 2012-02-20 23:21:17.70 UTC Parse QuickGO "proteinList" file format 2012-02-20 23:09:54.660 UTC Rafael C. Jimenez 2012-02-20 21:22:11.198 UTC 65c514d6-d7b1-44be-af29-1f5ec76173c5 2012-02-19 22:50:36.671 UTC f09568c5-4617-4ad1-a7da-eab0e4f3350d 2012-02-20 22:40:50.956 UTC 4d990e35-5f26-4c98-bb20-8db574499971 2012-02-20 21:24:11.725 UTC f699f0af-1e29-4419-bdd8-85281cf001f0 2012-02-20 23:20:10.758 UTC 24fde965-3770-4c10-a0f4-919ba249f52d 2012-02-20 23:14:10.417 UTC 9d81aafa-f875-419a-89f1-781ff803c7ef 2012-02-20 22:35:55.748 UTC ee83b6ea-549c-4ada-8fd6-8eec8e801cc5 2012-02-20 21:21:53.494 UTC 5f7bfa79-4c99-4593-a244-003f7a2541a5 2012-02-20 22:51:22.41 UTC bd2f222c-3793-47f4-9c7c-0b87d37f0613 2012-02-20 22:52:09.878 UTC Get_models_from_BioMUniProtId00 UniProt accession 2012-08-22 05:09:54.853 UTC P37173 2012-08-22 05:10:00.308 UTC BioModelsIds BIOMD0000000163 BIOMD0000000101 BIOMD0000000342 BIOMD0000000173 BIOMD0000000112 2012-08-22 05:11:15.14 UTC List of model identifiers from BioModels 2012-08-22 05:11:36.115 UTC SBMLBioModelsUrlgetModelsIdByUniprotIduniprotId0getModelsIdByUniprotIdReturn11net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivity http://www.ebi.ac.uk/biomodels-main/services/BioModelsWebServices?wsdl getModelsIdByUniprotId net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.WSDLActivity http://www.ebi.ac.uk/biomodels-main/services/BioModelsWebServices?wsdl getModelSBMLById net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.BeanshellActivity BiomodelsId 0 text/plain java.lang.String true BiomodelsUrl 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetModelsIdByUniprotIduniprotIdUniProtIdgetModelSBMLByIdidgetModelsIdByUniprotIdgetModelsIdByUniprotIdReturnGetBiomodelsUrlBiomodelsIdgetModelsIdByUniprotIdgetModelsIdByUniprotIdReturnBioModelsIdsgetModelsIdByUniprotIdgetModelsIdByUniprotIdReturnSBMLgetModelSBMLByIdgetModelSBMLByIdReturnBioModelsUrlGetBiomodelsUrlBiomodelsUrl efd8b80d-407a-4149-9826-93172f276f80 2012-08-24 02:17:34.386 UTC A 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 UTC c128c3c6-e35f-458c-8d79-aba048e6ec5a 2012-08-22 03:20:53.662 UTC f76fc0cc-05ae-4114-a07b-daf670d2cc34 2012-08-24 02:26:34.534 UTC 1634845c-4841-4b18-bd8a-649af1cc4ed3 2012-08-24 02:24:51.27 UTC a969986e-0f03-4619-af18-aab3b56397bd 2012-08-24 02:30:01.105 UTC 46f50814-730e-4ef4-87fd-d45f6798f0a3 2012-08-22 03:17:57.311 UTC Rafael C. Jimenez 2012-08-24 02:24:53.290 UTC Get models from BioModels including the input protein. 2012-08-24 02:24:45.720 UTC 487bd2d0-47a8-491b-ad50-c3f900de45fc 2012-08-22 06:03:15.88 UTC Get_a_list_of_proteins_from_a_Gene_Ontology__GO__termGeneOntologyId00 GO:0002080 2012-02-19 22:39:10.360 UTC Gene Ontology Id 2012-02-19 22:38:58.104 UTC TaxonomyId00 Taxonomy 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 UTC 9606 2012-02-19 22:39:24.72 UTC status 200 2012-02-19 22:49:52.211 UTC HTTP response status codes. http://en.wikipedia.org/wiki/List_of_HTTP_status_codes 2012-02-19 22:49:29.724 UTC listOfProteins DB 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 UTC Results in Tab Separated Values (TSV) 2012-02-19 22:44:03.860 UTC QuickGODatabase0Format0GoId0TaxId0status00responseBody00net.sf.taverna.t2.activitiesrest-activity1.4net.sf.taverna.t2.activities.rest.RESTActivity GET http://www.ebi.ac.uk/QuickGO/GAnnotation?goid={GoId}&db={Database}&format={Format}&tax={TaxId} text/tab-separated-values application/xml String false false false false false Format java.lang.String Database java.lang.String TaxId java.lang.String GoId java.lang.String net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.StringConstantActivity UniProtKB net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.StringConstantActivity proteinList net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeQuickGODatabaseDatabasevalueQuickGOFormatFormatvalueQuickGOGoIdGeneOntologyIdQuickGOTaxIdTaxonomyIdstatusQuickGOstatuslistOfProteinsQuickGOresponseBody 214af3fd-850d-467e-992a-4de0cb2670d3 2012-02-20 22:57:08.806 UTC 5bd1e0e9-30b9-4c72-a097-fbd2880221be 2012-02-20 21:35:41.916 UTC 4d990e35-5f26-4c98-bb20-8db574499971 2012-02-20 21:24:11.725 UTC 65c514d6-d7b1-44be-af29-1f5ec76173c5 2012-02-19 22:50:36.671 UTC Get a list of proteins from a Gene Ontology (GO) term 2012-02-20 21:23:15.307 UTC ee83b6ea-549c-4ada-8fd6-8eec8e801cc5 2012-02-20 21:21:53.494 UTC f70cfe42-70e5-44b8-a9e5-8e5a9add9779 2012-02-20 22:59:15.786 UTC Get a list of UniProt proteins that have been annotated with the same Gene Ontology (GO) term. This workflow use the the QuicGO service 2012-02-20 22:59:11.564 UTC Rafael C. Jimenez 2012-02-20 21:22:11.198 UTC