psidev-pi-dev

[Psidev-pi-dev] OMSSA usecase example

[Jennifer S. <jen...@ma...>]

Hi,

I have added two OMSSA usecase examples to the svn repository 
(http://code.google.com/p/psi-pi/source/browse/trunk/examples/schema_usecase_examples/working9July/).

I just have a small comment concerning modifications, I used cvParams 
when assigning a particular modification to a peptide however when 
adding the modifications that were used in the search I am not able to 
use cvParams instead it has this structure

<ModificationParams>
    <SearchModification fixedMod="false">
       <ModName unitName="MOD::00425" unitAccession="??" 
value="Oxidation (M)" />
       <MassValus unitName="" unitAccession="" value="" />
       <SpecificityRule....

I am not sure why we are not able to use cvParams or what I was supposed 
to put here?

Thanks,

Jenny

PS. I am afraid Julian and I will not be able to make the call later to day.

Re: [Psidev-pi-dev] OMSSA usecase example

[Martin E. <mar...@ru...>]

Hi Jenny, hi Andy, hi all!

>        <ModName unitName="MOD::00425" unitAccession="??" value="Oxidation (M)" />
>        <MassValus unitName="" unitAccession="" value="" />
>        <SpecificityRule....
> I am not sure why we are not able to use cvParams or what I was supposed
> to put here?
It is intended that these are derived from simpler FuGE types to avoid:
<ModName>
	<cvParam ... />
</ModName>
<MassValue>
	<cvParam ... />
</MassValue>

but indeed ModName seems to be wrongly derived from PropertyValue, because one cannot specifiy the accession attribute.

Andy, should be changed to be derived from CvParamType, isn't it?

Correct (hopefully):
 <ModName accession="MOD::00425" value="Oxidation (M)" />
 <MassValue value="15.9" unitName="Da" unitAccession="MOD::005XY"/>

  Bye
   Martin


> 
> Thanks,
> 
> Jenny
> 
> PS. I am afraid Julian and I will not be able to make the call later to day.
> 
> 
> 
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