Re: [Psidev-ms-dev] referenceableParamGroup

[Wilfred H T. <Ta...@ap...>]

After further investigation, I found that pwiz/SeeMS are indeed properly 
handling the referenceable param groups. Thanks to Matt Chambers for 
setting me straight!

My real problem was related to putting data into the proper place in the 
spectrum/spectrumDescription/scan/... hierarchy. A way to solve this 
problem was to replicate the referenceable param group reference 4(!!) 
times for each of the locations in the hierarchy where some data was 
required. A somewhat ugly solution, IMHO.

      <spectrum index="9" id="x1x1x4x1" nativeID="1.1.4.1" 
defaultArrayLength="5207">
        <referenceableParamGroupRef ref="Sample1Experiment1" />
        <spectrumDescription>
          <referenceableParamGroupRef ref="Sample1Experiment1" />
          <cvParam cvRef="MS" accession="MS:1000285" name="total ion 
current" value="86446" />
          <scan>
            <referenceableParamGroupRef ref="Sample1Experiment1" />
            <cvParam cvRef="MS" accession="MS:1000016" name="scan time" 
value="0.134683333333333" />
            <scanWindowList count="1">
              <scanWindow>
                <referenceableParamGroupRef ref="Sample1Experiment1" />
              </scanWindow>
            </scanWindowList>
          </scan>
        </spectrumDescription>

The validator, however, currently is NOT properly handling the 
referenceable param groups. I did a controlled experiment where 
information was written out (1) using referenceable param group 
references, or (2) writing out the actual data elements represented by the 
referenceable param group references. The validator does parse things 
properly for case (2) but not for case (1).

Thanks,
Wilfred




Matt Chambers <mat...@va...> 
Sent by: psi...@li...
08/13/2008 04:33 PM
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Re: [Psidev-ms-dev] referenceableParamGroup






A vile calumny! ;)

SeeMS, based on ProteoWizard, does properly recurse into referenceable 
param groups when they are actually referenced. If you were testing on 
the tiny2_pwiz.mzML file, it has referenceableParamGroups set up for 
common MS1 and MS2 params, but no other elements make a reference to 
them. It also has a rPG for common instrument params (model term and 
serial number), and that reference is resolved properly (hold the mouse 
over a the IC Id in the grid control to see it working in SeeMS). It's 
conceivable you've found a bug in pwiz though so please email me with 
details off-list if you're sure you're seeing improper behavior.

It is my understanding that the semantic validator uses a Java-based 
equivalent of ProteoWizard which also supports resolving references to 
param groups (i.e. checking in them when checking the term rules).

I agree though that rPG is a fantastic concept that may be 
undersupported. It's especially bad for writers which have the difficult 
task of coming up with the groups before writing the data containing the 
references to them. Since it's unlikely many writers will use them it 
follows that some reader implementors will be lazy and not support 
parsing them. That means there's even more reason to use a robust 
library implementation instead of reinventing the wheel. :)

-Matt


Wilfred H Tang wrote:
>
> The referenceableParamGroup concept is a fantastic idea, but I have 
> some reservations about using it when I'm writing out mzML data. I'm 
> concerned that not all mzML parsers will understand this fully, and 
> there's no mechanism to force mzML parsers to treat 
> referenceableParamGroup properly.
>
> For example:
>  - I tried loading a mzML file containing referenceableParamGroup 
> references into SeeMS, and the information contained in the 
> referenceableParamGroup references didn't show up at all (though it is 
> possible some other problem is causing the information to not get read 
> in properly).
>  - Does the validator parse referenceableParamGroup references when 
> checking that all the "musts" are present?
>
> Thanks,
> Wilfred


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