[MOBY-l] Taverna & MOBY services

[Twigger Simon]

I've managed to get the workflow doing something without breaking, Im a 
little hamstrung at the moment because Im using a Mac and for some 
reason I cant expand the processors in the advanced model explorer once 
I've assigned inputs and outputs - clicking with the mouse doesn't work 
so its hard to reroute things. (Tom Oinn had mentioned this was a 
'feature' a while ago - I'll try on XP tonight)

I need to add some more output objects to see if Im getting something 
sensible back out. I only linked the moby value to the one output 
object and its blank but I think thats because I have no value in my 
moby service output, I should try the namespace, etc. I suspect, just 
to test that things are happening. I'll explore the examples some more 
and go from there.

Thanks for everyone's advice, I think Im on my way.

Simon.

Here's the XML that comes back from the service when I do a test query 
with <Object namespace="" id="A2m"/>

<?xml version='1.0' encoding='UTF-8'?><moby:MOBY 
xmlns:moby='http://www.biomoby.org/moby' 
xmlns='http://www.biomoby.org/moby'><moby:mobyContent 
moby:authority='http://castor.brc.mcw.edu'>
         <moby:mobyData moby:queryID='1'>
             <moby:Simple moby:articleName=''>
                 <moby:text-plain moby:namespace="RGD" moby:id="A2m" 
articleName="geneSymbol"><CrossReference>

                         <Invocation namespace="" id="A2m"/>

                                 <Object namespace="PMID" id="89207509"/>
<Object namespace="PMID" id="2468362"/>
<Object namespace="PMID" id="21638024"/>
<Object namespace="PMID" id="11779202"/>

                                 <Object namespace="NCBI_Acc" 
id="M22670"/>
<Object namespace="NCBI_Acc" id="M23567"/>
<Object namespace="NCBI_Acc" id="J02635"/>
<Object namespace="NCBI_Acc" id="NM_012488"/>

                                 <Object namespace="NCBI_Acc" 
id="NP_036620"/>
<Object namespace="NCBI_Acc" id="AAA41592"/>
<Object namespace="NCBI_Acc" id="AAA77658"/>
<Object namespace="NCBI_Acc" id="AAA40636"/>

                                 <Object namespace="LocusID" id="24153"/>

                                 <Object namespace="Swiss-Prot" 
id="P06238"/>

                                 <Object namespace="TIGR_TGI" 
id="TC239648"/>
<Object namespace="TIGR_TGI" id="TC229016"/>

                         </CrossReference>
</moby:text-plain>
                 </moby:Simple>
         </moby:mobyData>
         </moby:mobyContent></moby:MOBY>


On Jan 20, 2005, at 4:49 PM, Martin Senger wrote:

>> Im trying to get a quick MOBY service up and running using Taverna and
>> its not working quite as I would like.
>>
>    The best would be to give me the name of your service (and perhaps 
> the
> registry where it can be found - unloess it is in the main Mark's
> registry) - and the input (in raw XML) that you would like to send to 
> that
> service. Then I will see what's happening, and perhaps I can find wher 
> is
> the problem.
>
>> text to the service it always fails, the stack trace in the terminal
>> seems to indicate a perl problem with an error thrown by XML::Parser
>>
>    That's why I would like to see the full (raw) XML you are sending to
> that service.
>
>> I noticed from Mark's last presentation that the taverna workflow 
>> shown
>> there seems to have two input objects (blue triangles) - presumably a
>> namespace and an ID that are going into a create_moby_data 'box'. Im
>> wondering if there is more to using MOBY via Taverna than a simple 
>> text
>> input object and that is my problem, or if its a more fundamental
>> service problem.
>>
>    Well, you can always send a raw XML to a moby service in taverna -
> withou using any of these blue triangles. The create-moby-data widget 
> is
> there only for simplest cases. The more complex input you have the more
> probably you need to create XML manually and send it as one input to
> taverna.
>
>    Cheers,
>    Martin
>
> -- 
> Martin Senger
>
> EMBL Outstation - Hinxton                Senger at EBI.ac.uk
> European Bioinformatics Institute        Phone: (+44) 1223 494636
> Wellcome Trust Genome Campus             (Switchboard:     494444)
> Hinxton                                  Fax  : (+44) 1223 494468
> Cambridge CB10 1SD
> United Kingdom                           
> http://industry.ebi.ac.uk/~senger
>
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>
--

Simon N. Twigger, Ph.D.
Assistant Professor, Department of Physiology
Medical College of Wisconsin
8701 Watertown Plank Road,
Milwaukee, WI, USA
tel: 414-456-8802
fax: 414-456-6595
AIM/iChat: simontatmcw