Chemical2URIsChem_name00 Can be the trivial name, SMILES, InChI, InChIKey, or Chemical Abstract Service number. 2015-08-18 14:49:51.128 UTC Retinoic acid 2015-08-18 14:49:56.946 UTC uri_out2Chemical_name_to_chemspider_IDToken0ChemicalNameOrID0CSIDs11 This workflow maps a chemical name to a ChemSpider identifier. 2015-08-18 14:47:38.290 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.InvokeTokenvalue00 The value should be your ChemSpider token. 2015-08-18 14:49:20.676 UTC net.sf.taverna.t2.activitiesstringconstant-activity1.5net.sf.taverna.t2.activities.stringconstant.StringConstantActivity your token here 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.InvokeWorkflow40id_in0mapped_uris11 This workflow maps a ChemSpider identifier to uniform resource identifiers using the Open PHACTS platform. 2015-08-18 14:48:16.891 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.InvokeChemical_name_to_chemspider_IDTokenTokenvalueChemical_name_to_chemspider_IDChemicalNameOrIDChem_nameWorkflow40id_inChemical_name_to_chemspider_IDCSIDsuri_outWorkflow40mapped_uris Chemical2URIs 2015-08-18 14:44:27.962 UTC f4f35d59-0220-4a45-b050-751a896a55e0 2015-08-18 14:48:18.997 UTC 623f3109-d7b4-44c6-a0c4-2b0124e43f25 2015-08-18 14:50:02.532 UTC c72f4ed0-5145-4343-b46b-e5b731a7de08 2015-04-10 09:36:20.285 UTC affff037-1aa4-4e26-a142-4760933a9d67 2015-04-10 09:47:14.582 UTC f98b1394-4405-4468-a26a-f320bd90fce6 2015-04-10 10:01:44.753 UTC This workflow will map a chemical name or identifier to uniform resource identifiers (URIs). First the ChemSpider web service is used to map the chemical name to a ChemSpider identifier, then the ChemSpider identifier is mapped to URIs via the Open PHACTS platform. 2015-08-18 14:46:22.729 UTC 2b23429c-f805-4bdf-a9fb-cd15f84fa0d5 2015-04-10 09:36:56.292 UTC f078815c-e639-4fb6-ba4c-b7dc5e7a3be7 2015-04-10 09:44:57.162 UTC Kristina Hettne and Eelke van der Horst 2015-08-18 14:43:46.464 UTC 2e96458a-2295-427c-b2c7-92b494788b94 2015-08-18 14:57:32.825 UTC 28b025e7-d020-468e-89a2-8f369ee2be73 2015-08-18 13:48:25.770 UTC c85aa525-6ed1-4551-92f8-4a65572efb07 2015-08-18 14:46:23.5 UTC f1e5240c-b14e-4b59-bdee-cea8aa8fbab0 2015-08-18 14:53:59.673 UTC 9f7440b0-548f-4525-8e38-54c01f100707 2015-08-18 14:09:50.878 UTC Chemical_name_to_chemspider_IDChemicalNameOrID00 Retinoic acid 2011-09-20 13:21:39.653 UTC Can be the trivial name, SMILES, InChI, InChIKey, or Chemical Abstract Service number. 2012-05-30 14:25:58.790 UTC Token00 Your token 2015-08-18 14:54:18.216 UTC Security token needed to query the services. Information about how to recieve a token can be find here: http://www.chemspider.com/help-create-a-chemspider-account.aspx 2015-08-18 14:40:12.177 UTC CSIDs1 5337 2015-08-18 14:42:34.345 UTC Returns the ChemSpider IDs associated with the input. 2012-05-30 14:26:38.333 UTC SimpleSearchparameters0parameters00 This service will query the ChemSpider database for the input name or identifier and return the ChemSpider identifier. 2015-08-18 14:41:57.353 UTC net.sf.taverna.t2.activitieswsdl-activity1.5net.sf.taverna.t2.activities.wsdl.WSDLActivity http://www.chemspider.com/Search.asmx?WSDL SimpleSearch 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.InvokeSimpleSearch_inputquery0token0output00net.sf.taverna.t2.activitieswsdl-activity1.5net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity query 0 'text/plain' false token 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="SimpleSearch" name="parameters" qname="{http://www.chemspider.com/}SimpleSearch"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="query" qname="{http://www.chemspider.com/}&gt;SimpleSearch&gt;query" /><s:basetype optional="true" unbounded="false" typename="string" name="token" qname="{http://www.chemspider.com/}&gt;SimpleSearch&gt;token" /></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.InvokeSimpleSearch_outputinput0SimpleSearchResult11net.sf.taverna.t2.activitieswsdl-activity1.5net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false SimpleSearchResult 1 l('text/plain') 1 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="SimpleSearchResponse" name="parameters" qname="{http://www.chemspider.com/}SimpleSearchResponse"><s:elements><s:arraytype optional="true" unbounded="false" wrapped="true" typename="ArrayOfInt" name="SimpleSearchResult" qname="{http://www.chemspider.com/}&gt;SimpleSearchResponse&gt;SimpleSearchResult"><s:elementtype><s:basetype optional="false" unbounded="false" typename="int" name="" qname="{http://www.w3.org/2001/XMLSchema}int" /></s:elementtype></s:arraytype></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.InvokeSimpleSearchparametersSimpleSearch_inputoutputSimpleSearch_inputqueryChemicalNameOrIDSimpleSearch_inputtokenTokenSimpleSearch_outputinputSimpleSearchparametersCSIDsSimpleSearch_outputSimpleSearchResult 91a055d7-16e2-4aea-87f6-9d8868494230 2015-08-18 14:41:57.503 UTC 4c9bdeb7-cdff-432f-98fe-db6cf58ee305 2011-09-20 15:49:53.11 UTC Chemical name to chemspider ID 2011-09-20 13:24:08.709 UTC 1079101b-cec7-471e-b0d7-3f0aca2429c4 2015-04-09 19:00:24.114 UTC Kristina Hettne 2011-09-20 13:23:51.287 UTC 4f05d0b1-0603-4eef-9f16-23a71184827f 2012-06-01 12:26:06.691 UTC c1870043-7462-4901-877f-6fe6b700b0da 2012-05-30 14:48:11.587 UTC 327d1442-d467-44fa-95d7-5bb37d8d1dbb 2012-06-01 12:33:19.662 UTC 4baed6ef-c1ba-469b-8cd2-cce674084566 2011-09-20 13:39:00.918 UTC 003ca301-aa6c-4d35-ad04-a97df8f3647f 2015-08-18 14:08:57.798 UTC 4d36b81c-76f0-44fb-ae84-6fa0ba3c0c39 2011-09-20 13:22:33.814 UTC 7875740c-d4cd-4313-bf69-e324a3fc4ee5 2015-08-18 14:42:37.182 UTC da175cb5-7493-49a5-bff5-b7b3d213e57f 2011-09-20 15:45:15.659 UTC 224a7f0b-75eb-481c-95bb-6b9cfff66e4e 2015-08-18 14:00:53.423 UTC 9364dbb2-c07f-46be-8041-0b5fa8fb81d0 2015-08-18 14:54:21.897 UTC CSID2OPSuriid_in00 2425 2015-08-18 14:31:56.6 UTC ChemSpider identifier 2015-08-18 14:32:15.956 UTC mapped_uris1 Unique resource identifiers mapped to the input ChemSpider identifier. 2015-08-18 14:32:59.351 UTC http://www.conceptwiki.org/concept/index/1a8fa9d2-b16b-4b8e-b511-5e976c644de0 2015-08-18 14:33:33.574 UTC REST_Serviceid0responseBody00 This implementation use the mapURI REST service that queries the Open PHACTS identity mapping service (IMS) for uniform resource identifiers mapped to a ChemSpider identifier. The APP_ID and APP_KEY variables in the URL Template field needs to be replaced with your Open PHACTS application id and key. They can be requested from here: https://dev.openphacts.org/login 2015-08-18 14:56:44.469 UTC net.sf.taverna.t2.activitiesrest-activity1.5net.sf.taverna.t2.activities.rest.RESTActivity GET https://beta.openphacts.org/1.4/mapUri?app_id=APP_ID&app_key=APP_KEY&Uri=http%3A%2F%2Fwww.chemspider.com%2F{id}&_format=xml application/xml application/xml String false false false false true id 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.InvokeXPath_Servicexml_text0nodelist11 The XPath service provides fast processing of XML data. 2015-08-18 14:30:40.501 UTC net.sf.taverna.t2.activitiesxpath-activity1.5net.sf.taverna.t2.activities.xpath.XPathActivity <?xml version="1.0" encoding="utf-8"?> <result format="linked-data-api" version="1.4" href="https://beta.openphacts.org/1.4/mapUri?app_id=3412d473&amp;app_key=56aa04973091c2a1fb235ad84cd9fdbd&amp;Uri=http%3A%2F%2Fwww%2Echemspider%2Ecom%2F597&amp;_format=xml"><primaryTopic href="http://www.chemspider.com/597"><exactMatch><item href="http://rdf.chemspider.com/597"/><item href="http://info.identifiers.org/chemspider/597"/><item href="http://purl.org/obo/owl/CHEBI#CHEBI_17822"/><item href="http://www.conceptwiki.org/web-ws/concept/get?uuid=a30fdee1-0b48-49a5-8bef-afefb03350d0"/><item href="http://purl.bioontology.org/ontology/MSH/C027794"/><item href="http://info.identifiers.org/mesh/D012694"/><item href="http://www.conceptwiki.org/concept/index/a30fdee1-0b48-49a5-8bef-afefb03350d0"/><item href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17822"/><item href="http://identifiers.org/chemspider/597"/><item href="http://info.identifiers.org/chebi/CHEBI:35243"/><item href="http://ops.rsc.org/OPS366770/rdf"/><item href="http://ops.rsc-us.org/OPS366770"/><item href="http://identifiers.org/chebi/CHEBI:17822"/><item href="http://bioportal.bioontology.org/ontologies/1351?p=terms&amp;conceptid=D012694"/><item href="http://identifiers.org/obo.chebi/CHEBI:17822"/><item href="http://www.ebi.ac.uk/ontology-lookup/?termId=CHEBI:35243"/><item href="http://ops.rsc.org/Compounds/Get/1769784"/><item href="http://bio2rdf.org/chebi:17822"/><item href="http://purl.obolibrary.org/obo/CHEBI_35243"/><item href="http://www.chemspider.com/597"/><item href="http://identifiers.org/mesh/D012694"/><item href="http://www.chemspider.com/Chemical-Structure.597.html"/><item href="http://bio2rdf.org/mesh:D012694"/><item href="http://bio2rdf.org/chebi:35243"/><item href="http://identifiers.org/chebi/CHEBI:35243"/><item href="http://www.chemspider.com/Chemical-Structure.597"/><item href="http://purl.bioontology.org/ontology/CHEBI/CHEBI:35243"/><item href="http://identifiers.org/mesh/C027794"/><item href="http://www.conceptwiki.org/concept/a30fdee1-0b48-49a5-8bef-afefb03350d0"/><item href="http://purl.bioontology.org/ontology/MSH/D012694"/><item href="http://ops.rsc.org/Compounds/Get/366770"/><item href="http://purl.obolibrary.org/obo/CHEBI_17822"/><item href="http://www.ebi.ac.uk/ontology-lookup/?termId=CHEBI:17822"/><item href="http://ops.rsc.org/OPS366770"/><item href="http://ops.rsc.org/OPS1769784"/><item href="http://identifiers.org/obo.chebi/CHEBI:35243"/><item href="http://bio2rdf.org/mesh:C027794"/><item href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:35243"/><item href="http://www.chemspider.com/Chemical-Structure.597.rdf"/><item href="http://info.identifiers.org/mesh/C027794"/><item href="http://ops.rsc.org/OPS1769784/rdf"/><item href="http://ops.rsc-us.org/OPS1769784"/><item href="http://purl.org/obo/owl/CHEBI#CHEBI_35243"/><item href="http://bioportal.bioontology.org/ontologies/1351?p=terms&amp;conceptid=C027794"/><item href="http://info.identifiers.org/chebi/CHEBI:17822"/><item href="http://purl.bioontology.org/ontology/CHEBI/CHEBI:17822"/></exactMatch></primaryTopic><extendedMetadataVersion href="https://beta.openphacts.org/1.4/mapUri?app_id=3412d473&amp;app_key=56aa04973091c2a1fb235ad84cd9fdbd&amp;Uri=http%3A%2F%2Fwww%2Echemspider%2Ecom%2F597&amp;_format=xml&amp;_metadata=all%2Cviews%2Cformats%2Cexecution%2Cbindings%2Csite"/><definition href="https://beta.openphacts.org/api-config"/></result> /result/primaryTopic/exactMatch/item/@href 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_Serviceidid_inXPath_Servicexml_textREST_ServiceresponseBodymapped_urisXPath_Servicenodelist CSID2OPSuri 2015-08-18 14:34:51.119 UTC 808ffbd3-f186-4edf-83ad-2336054ae42f 2015-08-18 14:56:44.583 UTC dc844961-6060-4366-b088-8476a11fb044 2015-04-10 09:55:32.437 UTC e3f1b74e-43d1-4d06-9489-c6e86ff2c5fc 2015-08-18 14:33:33.702 UTC 5d2b7282-7282-45b4-b6bc-d21ea5eccc64 2015-04-10 10:00:41.334 UTC This workflow uses the mapURI REST service to map a ChemSpider identifier to uniform resource identifiers from the Open PHACTS platform. NOTE: The APP_ID and APP_KEY variables in the URL Template field needs to be replaced with your Open PHACTS application id and key. They can be requested from here: https://dev.openphacts.org/login 2015-08-18 14:57:00.357 UTC 242e5a67-36a2-49ac-9b1d-3dbfc1315f51 2015-04-10 09:50:20.561 UTC 115e44da-11e4-4fb6-a62e-b8b7f47c5cf2 2015-08-18 14:57:01.992 UTC 54b50c02-f1fc-4bfb-9ab1-ec053ec33fa2 2015-08-18 14:30:11.614 UTC 0df3fea9-f686-411a-b285-6cd6bb5c60e2 2015-08-18 14:36:37.461 UTC aa8c1e03-377c-4f1c-9789-7666c0afbcca 2015-08-18 14:38:03.479 UTC 62d6140b-0e10-47e2-971c-5a3fe888845e 2015-04-10 09:57:16.631 UTC Kristina Hettne and Eelke van der Horst 2015-08-18 14:34:01.768 UTC