[MOBY] [MOBY-l] Interpreting results from Service->execute()

[José María Fernández González]

> Hi MOBYers,
> 
> I've been playing with MOBY all day (installed Perl 5.8.3 just for this!), and find that it works pretty well. I've successfully called plantspGetProtein from sdsc.edu and GetPubmed from prometheus.brc.mcw.edu.
> 
> Now I'm trying to call getInteractingMethods from pdg.cnb.uam.es, and although it returns something, I just don't understand what it returns. The code I'm using to call it is appended at the end of this (having been cribbed from
> Catherine Letondal and Ken Streube - thanks to both for great tutorials!), but the important part is this:
> 
>    my $pid = "EBI-141";
>    my $result =
>       $service->execute( XMLinputlist => [
>                                           ["object$i",
>                                            "<Object namespace='IntAct' id='$pid'/>"]
>                                          ] ) || 'None';

The shortest answer is: there is no answer. (please, follow reading!)

The larger one: EBI-141 is an IntAct identifier, which corresponds to an 
interactor in this case (P53905 from UniProt).

The service was designed thinking on protein ids because we are 
integrating data both from IntAct and other sources (like REGIA or 
VPiL). So, the identifier is not found and the method returns nothing... 
Also, it doesn't belong to any of the accepted input namespaces 
(AGI_LocusCode, Swiss-Prot, SPTR, TrEMBL)

But it is true, there are two bugs: one related to signal an invalid 
namespace, and other related to say 'no output'. I'm fixing them since now.

> 
> 
> The simpler answer might be that the service isn't working properly ;-) 
> We'll have to ask our Spanish friends to check it... hopefully they are
> listening!

You had enough luck (at least this time ;-)!

> 
> good luck!
> 
> Mark
> 
> 

	Cheers,
		José María


-- 
José María Fernández González		e-mail: jmfernandez at cnb.uam.es
Tlfn:	(+34) 91 585 46 69		Fax:	(+34) 91 585 45 06
Grupo de Diseño de Proteinas		Protein Design Group
Centro Nacional de Biotecnología	National Center of Biotechnology
C.P.: 28049				Zip Code: 28049
Campus Universidad Autónoma. Cantoblanco, Madrid (Spain).