Hi I am trying to get PDB IDs and Pathways image for a given identifier
but its not returning any results for these two.Please let me know what i am
missing on this workflow.I would appreciate all help .My inputs were :Namespace
: NCBI_giid:210031822 and 132814489RegardsRinku
<?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:b6b0b261-44d5-40b4-93f9-d11a9b3c32d0"
author="" title="workflow1" />
<s:processor name="Decode_base64_to_byte">
<s:local>org.embl.ebi.escience.scuflworkers.java.DecodeBase64</s:local>
</s:processor>
<s:processor name="Parse_Moby_Data_Object3">
<s:description>Processor to parse the datatype Object</s:description>
<s:biomobyparser>
<s:endpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</s:endpoint>
<s:datatype>Object</s:datatype>
<s:articleName>gos</s:articleName>
<s:description>Processor to parse the datatype Object</s:description>
</s:biomobyparser>
</s:processor>
<s:processor name="Parse_Moby_Data_Object">
<s:description>Processor to parse the datatype Object</s:description>
<s:biomobyparser>
<s:endpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</s:endpoint>
<s:datatype>Object</s:datatype>
<s:articleName>pathways</s:articleName>
<s:description>Processor to parse the datatype Object</s:description>
</s:biomobyparser>
</s:processor>
<s:processor name="ID2GO">
<s:description>Maps an database identifier to its GO terms</s:description>
<s:biomobywsdl>
<s:mobyEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</s:mobyEndpoint>
<s:serviceName>ID2GO</s:serviceName>
<s:authorityName>mpiz-koeln.mpg.de</s:authorityName>
</s:biomobywsdl>
</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="ID2PMID">
<s:description>Maps a database identifier to its PubMedIDs</s:description>
<s:biomobywsdl>
<s:mobyEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</s:mobyEndpoint>
<s:serviceName>ID2PMID</s:serviceName>
<s:authorityName>mpiz-koeln.mpg.de</s:authorityName>
</s:biomobywsdl>
</s:processor>
<s:processor name="getKeggPathwayAsGif">
<s:description>This service, given a KEGG pathway, returns a Gif image of
the pathway if it exists.
For example, the <Object, KEGG_PATHWAY, 'hsa00053')
returns a diagram of the pathway 'ASCORBATE AND ALDRATE
METABOLISM'.</s:description>
<s:biomobywsdl>
<s:mobyEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</s:mobyEndpoint>
<s:serviceName>getKeggPathwayAsGif</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:processor name="MOBYSHoundGetGenBankFasta">
<s:description>consumes a NCBI_Acc, NCBI_gi, PIR, SwissProt, Embl,
or PDB identifier and returns the equivalent genbank record as a
FASTA object</s:description>
<s:biomobywsdl>
<s:mobyEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</s:mobyEndpoint>
<s:serviceName>MOBYSHoundGetGenBankFasta</s:serviceName>
<s:authorityName>bioinfo.icapture.ubc.ca</s:authorityName>
</s:biomobywsdl>
</s:processor>
<s:processor name="MOBYSHoundGetGenBankff">
<s:description>consumes a NCBI_Acc, NCBI_gi, PIR, SwissProt, Embl,
or PDB identifier and returns the equivalent genbank record as a
genbank-flatfile object</s:description>
<s:biomobywsdl>
<s:mobyEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</s:mobyEndpoint>
<s:serviceName>MOBYSHoundGetGenBankff</s:serviceName>
<s:authorityName>bioinfo.icapture.ubc.ca</s:authorityName>
</s:biomobywsdl>
</s:processor>
<s:processor name="Object">
<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="Parse_Moby_Data_b64_encoded_gif">
<s:description>Processor to parse the datatype
b64_encoded_gif</s:description>
<s:biomobyparser>
<s:endpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</s:endpoint>
<s:datatype>b64_encoded_gif</s:datatype>
<s:articleName>image</s:articleName>
<s:description>Processor to parse the datatype
b64_encoded_gif</s:description>
</s:biomobyparser>
</s:processor>
<s:processor name="Parse_Moby_Data_Object1">
<s:description>Processor to parse the datatype Object</s:description>
<s:biomobyparser>
<s:endpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</s:endpoint>
<s:datatype>Object</s:datatype>
<s:articleName>pmids</s:articleName>
<s:description>Processor to parse the datatype Object</s:description>
</s:biomobyparser>
</s:processor>
<s:processor name="Parse_Moby_Data_FASTA">
<s:description>Processor to parse the datatype FASTA</s:description>
<s:biomobyparser>
<s:endpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</s:endpoint>
<s:datatype>FASTA</s:datatype>
<s:articleName>fasta</s:articleName>
<s:description>Processor to parse the datatype FASTA</s:description>
</s:biomobyparser>
</s:processor>
<s:processor name="Parse_Moby_Data_genbank_flatfile">
<s:description>Processor to parse the datatype
genbank-flatfile</s:description>
<s:biomobyparser>
<s:endpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</s:endpoint>
<s:datatype>genbank-flatfile</s:datatype>
<s:articleName>file</s:articleName>
<s:description>Processor to parse the datatype
genbank-flatfile</s:description>
</s:biomobyparser>
</s:processor>
<s:processor name="convertKeggGeneId2PDBId">
<s:description>This service consumes an identifier under the KEGG
namespace.
This identifier is then queried against the KEGG DB and all PDB records are
returned.</s:description>
<s:biomobywsdl>
<s:mobyEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</s:mobyEndpoint>
<s:serviceName>convertKeggGeneId2PDBId</s:serviceName>
<s:authorityName>bioinfo.icapture.ubc.ca</s:authorityName>
</s:biomobywsdl>
</s:processor>
<s:link source="Id" sink="Object:id" />
<s:link source="namaspace" sink="Object:namespace" />
<s:link source="ID2GO:Object(Collection - 'gos' As Simples)"
sink="Parse_Moby_Data_Object3:mobyData('Object')" />
<s:link source="ID2PMID:Object(Collection - 'pmids' As Simples)"
sink="Parse_Moby_Data_Object1:mobyData('Object')" />
<s:link source="MOBYSHoundGetGenBankFasta:FASTA(fasta)"
sink="Parse_Moby_Data_FASTA:mobyData('FASTA')" />
<s:link source="MOBYSHoundGetGenBankff:genbank-flatfile(file)"
sink="Parse_Moby_Data_genbank_flatfile:mobyData('genbank-flatfile')" />
<s:link source="Object:mobyData" sink="ID2GO:Object(id)" />
<s:link source="Object:mobyData" sink="ID2PMID:Object(id)" />
<s:link source="Object:mobyData"
sink="MOBYSHoundGetGenBankFasta:Object(identifier)" />
<s:link source="Object:mobyData"
sink="MOBYSHoundGetGenBankff:Object(identifier)" />
<s:link source="Object:mobyData"
sink="convertIdentifier2KeggID:Object(identifier)" />
<s:link source="convertIdentifier2KeggID:Object(keggID)"
sink="convertKeggGeneId2PDBId:Object(kegg_gene)" />
<s:link source="Decode_base64_to_byte:bytes" sink="pathwaysimage" />
<s:link source="Parse_Moby_Data_FASTA:fasta_'content'" sink="FASTA" />
<s:link source="Parse_Moby_Data_Object1:id" sink="PMID" />
<s:link source="Parse_Moby_Data_Object3:id" sink="GOID" />
<s:link source="Parse_Moby_Data_Object:id" sink="Pathways" />
<s:link source="Parse_Moby_Data_b64_encoded_gif:image_'content'"
sink="Decode_base64_to_byte:base64" />
<s:link source="Parse_Moby_Data_genbank_flatfile:file_'content'" sink="NCBI
sequence informantion" />
<s:link source="convertIdentifier2KeggID:Object(keggID)"
sink="getKeggPathwaysByKeggID:Object(keggID)" />
<s:link source="convertKeggGeneId2PDBId:Object(Collection - 'pdb_ids' As
Simples)" sink="PDBID" />
<s:link source="getKeggPathwayAsGif:b64_encoded_gif(image)"
sink="Parse_Moby_Data_b64_encoded_gif:mobyData('b64_encoded_gif')" />
<s:link source="getKeggPathwaysByKeggID:Object(Collection - 'pathways' As
Simples)" sink="Parse_Moby_Data_Object:mobyData('Object')" />
<s:link source="getKeggPathwaysByKeggID:Object(Collection - 'pathways' As
Simples)" sink="getKeggPathwayAsGif:Object(pathway)" />
<s:source name="namaspace" />
<s:source name="Id" />
<s:sink name="NCBI sequence informantion" />
<s:sink name="FASTA" />
<s:sink name="Pathways" />
<s:sink name="PMID" />
<s:sink name="PDBID" />
<s:sink name="GOID" />
<s:sink name="pathwaysimage" />
</s:scufl>
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