Re: [Psidev-ms-dev] mzML's binary arrays

[Marc S. <st...@in...>]

Hi Matt,
> I can't think of any notable semantic difference between userParams and 
> cvParams with uncontrolled string values. In both cases, you would have 
> to deal with an extra term that only your algorithm and its downstream 
> users know about. In both cases, the extra algorithm-specific arrays are 
> unusable for other tools (except ones you make of course or that are 
> made specifically to work with it). In both cases, the uncontrolled 
> string value cannot be relied on except in very controlled circumstances.
>   
That's not entirely true in my opinion. We have a small command line 
tool that can display statistics about these arrays.
Without a defined way to give the array a name the statistics would look 
like that:

array 0:
  min: 234
  max: 435435
  avg: 4545
array 1:
  min: 234
  max: 435435
  avg: 4545

With a defined way of naming arrays it would look like that:

array 'some descritpion of the array content 1':
  min: 234
  max: 435435
  avg: 4545
array 'some descritpion of the array content 2':
  min: 234
  max: 435435
  avg: 4545

At least to me the second alternative looks much better. Of cause we can 
store the name in the userParam 'name'.
But other tools would store it in the userParam 'Name' or 'custom_name' 
or 'custom name' ...
I really think there should be a controlled way to give an array a 
user-defined name.
There was a way in mzData (optional XML attribute 'name') and it's a 
step back not to have one in mzML.

> However, if your peak picking algorithm is versioned, it's exactly the 
> kind of thing we want in the CV. We want a term to briefly describe the 
> algorithm (which would go in dataProcessing) and also terms to describe 
> the parameters that a user can set. At the same time, CV terms for your 
> custom extra arrays could be added as well.
>   
We'll compile a list of the TOPP tools with short descriptions and post 
it on this mailing list.
The parameters will most likely not be included as the current count of 
parameters for all tools is 538 and they might change from release to 
release.

Best,
  Marc