Re: [Psidev-ms-dev] CV param readability

[Joshua T. <jt...@sy...>]

Hi Darren,

Speaking only for myself, I think that the "name" attribute should be optional in the file and not interfere with validation.  I've never understood why the text string needs to exactly match the CV for validation; someone one the list had brought up other languages, etc.  But I think it came up on the list before, and requiring strict mapping between accession numbers and text string seemed to be important for the format.  

At the least, acronyms would require additional 'mapping files' or something similar to be added to the specification, and the validator to be updated.  Maybe someone more familiar with these tasks could step in.  Maybe the CV could be expanded so that every entry had an additional "acronym" field.  This brings up other questions, like would uniqueness be enforced, etc?

Josh


Kessner, Darren E. wrote:
> I would like to propose using standard acronyms in the CV term names 
> when it is clear what they mean.
> 
>  
> 
> We currently have:
> 
> <cvParam cvLabel="MS" accession="MS:1000075" name="matrix assisted laser 
> desorption ionization" value=""/>
> 
> <cvParam cvLabel="MS" accession="MS:1000079" name="fourier transform ion 
> cyclotron resonance mass spectrometer" value=""/>
> 
>  
> 
> I think this is more readable:
> 
> <cvParam cvLabel="MS" accession="MS:1000075" name="MALDI" value=""/>
> 
> <cvParam cvLabel="MS" accession="MS:1000079" name="FT-ICR MS" value=""/>
> 
>  
> 
> The full name can still be available in the term description field.
> 
>  
> 
> I have an ulterior motive for this -- in the code generation of the 
> MSData library, the above terms become constants:
> 
>     MS_matrix_assisted_laser_desorption_ionization = 1000075,
> 
>     MS_fourier_transform_ion_cyclotron_resonance_mass_spectrometer = 
> 1000079,
> 
>  
> 
> But I think the following is more programmer-friendly:
> 
>     MS_MALDI = 1000075,
> 
>     MS_FT_ICR_MS = 1000079,
> 
>  
> 
>  
> 
>  
> 
> Darren
> 
>  
> 
>  
> 
>  
> 
> Darren Kessner
> 
> Scientific Programmer
> 
> Dar...@cs... <mailto:Dar...@cs...>
> 
> 310-423-9538
> 
>  
> 
> Spielberg Family Center for Applied Proteomics
> 
> Cedars-Sinai Medical Center
> 
> http://www.sfcap.cshs.org/
> 
>  
> 
>  
> 
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