[Psidev-pi-dev] Issue 42 in psi-pi: Issues with the CV

[<cod...@go...>]

Comment #56 on issue 42 by matthew....@vanderbilt.edu: Issues with the CV
http://code.google.com/p/psi-pi/issues/detail?id=42

Yes, I was at that meeting too. :) The one (important, IMO) use case we did  
not
consider at that time is output of analysisXML without a corresponding mzML  
document.
In such a case, the mzML arbitrary id does not exist, but the nativeID  
does. This
fact convinces me that nativeID is a better reference than the arbitrary id.

The change of attribute name to nativeID is not so critical, but I think  
the risk of
confusing the spectrumID with the id attribute when it actually points to  
the
nativeID attribute is worse than the risk of confusing the nativeID  
attribute with
some property of the search engine. I think the documentation for the  
nativeID
attribute can easily make it clear what it's supposed to reference,  
especially since
it's on a spectrum-centric element; you can copy it from the mzML schema  
(although I
think this documentation could be improved upon):
<xs:documentation>The native identifier for the spectrum, used by the  
acquisition
software.</xs:documentation>

It's good to know about the header information. The nativeID (or whatever  
it's called
in analysisXML) format term would go in the spectra input definition as a  
CV Param
required by the mapping file.

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