Re: [Psidev-ms-dev] Some additional 'Unknown instrument' CV parameter thoughts

[Matthew C. <mat...@va...>]

Lennart Martens wrote:
> Hi Matt, and Colleagues,
>
>
>   
>> I don't really prefer one to the other very much, but I don't see how 
>> the parent term would be easier to validate ("all but X children of a 
>> term" doesn't make sense to me, do you mean "all children of a term 
>> except X"?)
>>     
>
> You are right; I provided bad shorthand for: 'all children of a term, 
> except X (and Y, and Z, ... -- potentially).
>
> The reason why it it is easier to validate is due to the way the 
> validator mapping file is designed, e.g. (example verbatim from current 
> 0.99.1 mapping file):
>
> 	    <CvTerm termAccession="MS:1000031" useTerm="false" 
> termName="instrument model" isRepeatable="false" 
> scope="/mzML/instrumentList/instrument" allowChildren="true" 
> cvIdentifier="MS"></CvTerm>
>
> this means that although all children of term 'MS:1000031 -- instrument 
> model' are allowed (allowChildren="true"), the term itself is not 
> allowed (useTerm="false"). By flipping this latter boolean, we can allow 
> the parent term, thus separating between MIAPE requirements (current 
> configuration) and the 'usable mzML requirements' (flipped boolean as 
> explained above) -- for the instrument model at least.
>   
OK, so it's an implementation thing. That's fine.

>> What about data converted from DTAs or MGFs 
>> where the user doesn't even remember (or never knew) what kind of 
>> instrument it came from?
>>     
>
> When the instrument is really unknown (which is unfortunate and 
> constitutes dramatic metadata loss whichever way you look at it), the 
> proposed scenario (usage of toplevel term) provides solace. For all 
> other scenarios (where an incentive to adapt convertor software or 
> report the development of a new instrument is concerned), the relative 
> obscurity of the 'fix' might contribute to 'going the extra mile' 
> (upgrading the convertor, mailing in the new instrument name).
>   
While the toplevel term does provide some solace, it is obscure enough 
that a casual user might look at it and think that something was wrong 
because it does not intuitively make sense for the category to appear as 
a value. What about this alternative: provide an "unknown instrument" 
term with a unique accession #, but make the term name something like 
"unknown (instrument type not specified or not in CV)". That would be 
intuitive but still eye-catching (and it would be the eye-catching part 
that implementors would want to minimize, because it makes them look 
bad). ;)

-Matt