Hi Iam trying to create this workflow where:a)the input will be a
identifier(currently it is gen bank acc number) and b)output will
be pathways associated with the accession number.When I give a
input for a gene accession number it fails eg:L78833Would you please
suggest what is wrong.I am very new to taverna and trying to know more of it by
creating workflows.Thanks a lot in advanceThanksRinku
<?xml version="1.0" encoding="UTF-8"?>
<s:scufl xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"; version="0.2"
log="0">
<s:workflowdescription
lsid="urn:lsid:net.sf.taverna:wfDefinition:b0e2f5a9-9370-4f02-b049-72badaa44051"
author="" title="pathwaysand proteinID" />
<s:processor name="identifier" boring="true">
<s:stringconstant>NCBI_AccVer</s:stringconstant>
</s:processor>
<s:processor name="CreateMobyObject">
<s:description>an object</s:description>
<s:biomobyobject>
<s:mobyEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</s:mobyEndpoint>
<s:serviceName>Object</s:serviceName>
<s:authorityName />
</s:biomobyobject>
</s:processor>
<s:processor name="convertIdentifier2KeggID">
<s:description>This service consumes an identifier from the following
namespaces: NCBI_gi, GenBank, UniProt, UniGene, PMID or OMIM and returns a KEGG
identifier that represents the KEGG id mapped to the input identifier.
An example input would be (in <Object, ns, id> triple format,
<Object, omim, 153240></s:description>
<s:biomobywsdl>
<s:mobyEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</s:mobyEndpoint>
<s:serviceName>convertIdentifier2KeggID</s:serviceName>
<s:authorityName>bioinfo.icapture.ubc.ca</s:authorityName>
</s:biomobywsdl>
</s:processor>
<s:processor name="getKeggPathwaysByKeggID">
<s:description>This service, given a KEGG identifier, attempts to retrieve
KEGG pathways that that contain this ID.
For example, passing in:
hsa:6402
results in the following pathway returned: hsa04514.</s:description>
<s:biomobywsdl>
<s:mobyEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</s:mobyEndpoint>
<s:serviceName>getKeggPathwaysByKeggID</s:serviceName>
<s:authorityName>bioinfo.icapture.ubc.ca</s:authorityName>
</s:biomobywsdl>
</s:processor>
<s:link source="id" sink="CreateMobyObject:id" />
<s:link source="namespace" sink="CreateMobyObject:namespace" />
<s:link source="CreateMobyObject:mobyData"
sink="convertIdentifier2KeggID:Object(identifier)" />
<s:link source="convertIdentifier2KeggID:Object(keggID)"
sink="getKeggPathwaysByKeggID:Object(keggID)" />
<s:link source="getKeggPathwaysByKeggID:Object(Collection - 'pathways')"
sink="keggpathway" />
<s:link source="identifier:value" sink="CreateMobyObject:namespace" />
<s:source name="id" />
<s:source name="namespace" />
<s:sink name="outputid" />
<s:sink name="keggpathway" />
</s:scufl>
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