Rinku Saha wrote:
Hi
I was trying to run this
workflow http://www.myexperiment.org/workflows/249 in taverna1.7 with
input as 9879(which is a PMID) and whatizitSissprot .But it didnot
return any results.
I would appreciate any help on this.
Looking at the equivalent website
http://www.ebi.ac.uk/webservices/whatizit/info.jsf it seems that to get
the form to work, you now need to specify that (under 2) the text is "A
list of PMIDs".
If you try 9879 in the form with "Plain Text" then it does not return
any useful results. Once it is changed to "A list of PMIDs" then it
does return information.
In the workflow, you need to change from using the contact operation to
the queryPmid one. See attached workflow where the queryPmid returns
results for 9879 and whatizitSwissprot
Regards
Rinku
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Alan
<?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:ad7e8c0b-b602-4004-ab94-3f96a65bef73" author="Hamish McWilliam" title="EBI_Whatizit">Perform a text-mining analysis of an input text document using the EBI's Whatizit tool (http://www.ebi.ac.uk/webservices/whatizit/info.jsf).
Whatizit provides a number of text-mining pipelines which can can detect various terms of biological interest in text documents. For example finding gene names and mapping them to UniProtKB identifiers, finding chemical terms and mapping them to ChEBI, etc.</s:workflowdescription>
<s:processor name="Unwrap_result">
<s:description>Unwrap the XML result.</s:description>
<s:local>
org.embl.ebi.escience.scuflworkers.java.XMLOutputSplitter
<s:extensions>
<s:complextype optional="false" unbounded="false" typename="contactResponse" name="parameters" qname="{http://www.ebi.ac.uk/webservices/whatizit/ws}contactResponse";>
<s:elements>
<s:basetype optional="true" unbounded="false" typename="string" name="return" qname="contactResponse>return" />
</s:elements>
</s:complextype>
</s:extensions>
</s:local>
</s:processor>
<s:processor name="Input_params">
<s:description>Build the input parameters data structure. Wraps the Whatizit pipeline name and the text document.</s:description>
<s:local>
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
<s:extensions>
<s:complextype optional="false" unbounded="false" typename="contact" name="parameters" qname="{http://www.ebi.ac.uk/webservices/whatizit/ws}contact";>
<s:elements>
<s:basetype optional="true" unbounded="false" typename="string" name="pipelineName" qname="contact>pipelineName" />
<s:basetype optional="true" unbounded="false" typename="string" name="text" qname="contact>text" />
<s:basetype optional="false" unbounded="false" typename="boolean" name="convertToHtml" qname="contact>convertToHtml" />
</s:elements>
</s:complextype>
</s:extensions>
</s:local>
</s:processor>
<s:processor name="contact">
<s:description>Process an input text document using a Whatizit pipeline.</s:description>
<s:arbitrarywsdl>
<s:wsdl>http://www.ebi.ac.uk/webservices/whatizit/ws?wsdl</s:wsdl>
<s:operation>contact</s:operation>
</s:arbitrarywsdl>
</s:processor>
<s:processor name="queryPmid">
<s:arbitrarywsdl>
<s:wsdl>http://www.ebi.ac.uk/webservices/whatizit/ws?wsdl</s:wsdl>
<s:operation>queryPmid</s:operation>
</s:arbitrarywsdl>
</s:processor>
<s:processor name="parametersXML">
<s:local>
org.embl.ebi.escience.scuflworkers.java.XMLOutputSplitter
<s:extensions>
<s:complextype optional="false" unbounded="false" typename="queryPmidResponse" name="parameters" qname="{http://www.ebi.ac.uk/webservices/whatizit/ws}queryPmidResponse";>
<s:elements>
<s:basetype optional="true" unbounded="false" typename="string" name="return" qname="queryPmidResponse>return" />
</s:elements>
</s:complextype>
</s:extensions>
</s:local>
</s:processor>
<s:processor name="parametersXML1">
<s:local>
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
<s:extensions>
<s:complextype optional="false" unbounded="false" typename="queryPmid" name="parameters" qname="{http://www.ebi.ac.uk/webservices/whatizit/ws}queryPmid";>
<s:elements>
<s:basetype optional="true" unbounded="false" typename="string" name="pipelineName" qname="queryPmid>pipelineName" />
<s:basetype optional="true" unbounded="false" typename="string" name="pmid" qname="queryPmid>pmid" />
</s:elements>
</s:complextype>
</s:extensions>
</s:local>
</s:processor>
<s:link source="Analysis_pipeline" sink="Input_params:pipelineName" />
<s:link source="Analysis_pipeline" sink="parametersXML1:pipelineName" />
<s:link source="Input_params:output" sink="contact:parameters" />
<s:link source="Text" sink="Input_params:text" />
<s:link source="Text" sink="parametersXML1:pmid" />
<s:link source="contact:parameters" sink="Unwrap_result:input" />
<s:link source="parametersXML1:output" sink="queryPmid:parameters" />
<s:link source="Unwrap_result:return" sink="Whatizit_result" />
<s:link source="parametersXML:return" sink="pmid_output" />
<s:link source="queryPmid:parameters" sink="parametersXML:input" />
<s:source name="Analysis_pipeline">
<s:metadata>
<s:description>Name of the Whatizit text-mining pipeline to use. For example: whatizitSwissprot
See the results of the getPipelinesStatus() method for a complete list of the available pipelines and their status.</s:description>
</s:metadata>
</s:source>
<s:source name="Text">
<s:metadata>
<s:description>Input text to process.
For example: NPY, BRCA1, Brca2 and Ca2</s:description>
</s:metadata>
</s:source>
<s:sink name="Whatizit_result">
<s:metadata>
<s:mimeTypes>
<s:mimeType>text/xml</s:mimeType>
</s:mimeTypes>
<s:description>Whatizit analysis result.</s:description>
</s:metadata>
</s:sink>
<s:sink name="pmid_output" />
</s:scufl>
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