Re: [Psidev-ms-dev] dataProcessing

[Marc S. <stu...@gm...>]

Hi Eric,

thanks for your reply.
When you want to allow both ordered and unordered processing steps, it 
all makes sense.
I thought everything should be ordered.

Regards,
  Marc

Eric Deutsch wrote:
> Hi Marc, below:
>
>   
>> From: psi...@li...
>>     
> [mailto:psidev-ms-dev-
>   
>> Hi all,
>>
>> i have problems understanding how the data processing part of the
>>     
> schema
>   
>> is intended.
>> The main question I have is: what does the "order" attribute define?
>> Is it the order of different tools that were applied or the order of
>> several processing steps done by the same software?
>>     
>
> It is the order of processing steps applied to the dataset over its
> journey from mass spec to current form.
>
>   
>> As it is under "processingMethod", I thought it defines the order of
>> several processing steps done by the same software.
>> However the terms "data processing action" and "file format
>>     
> conversion"
>   
>> should not be repeatable in this case.
>> Otherwise the order is undefined again.
>>     
>
> I don't understand what you mean by this. It would seem entirely
> possible for vendor software A to perform some thresholding first and
> write out data in thresholded profile mode. Then perhaps FOSS software B
> might be used to convert to mzML. Then some other program might be used
> to centroid the data and write out another mzML file. These might be 3
> softwares used in the history of the data with order 1, 2, 3,
> respectively.
>
>   
>> When i looked into the tiny1 example, it confused me even more.
>>     
>
> In this case there are several algorithms applied in the same step since
> it is not known precisely in what order they were performed. So in the
> example, first Xcalibur was used to perform deisotoping, charge
> deconvolution, and peak picking. These are all lumped together as step
> 1. Perhaps they are result of a single algorithm or action and not
> separatable. Or perhaps there should be some inherent order, but it is
> not know to the writer. Then step 2 is the conversion to mzML. If the
> order of deisotoping, charge deconvolution, and peak picking is
> specifically known and relevant, it would be permissible to write this
> is a 4-step process, with order 1, 2, 3, and 4.
>
> Has this answered your question? Or perhaps I have misunderstood your
> confusion? If this clears it up, I will update the documentation to
> reflect this description.
>
> Also, if any of the other designers feel I have not described the intent
> correctly, please speak up!
>
> Regards,
> Eric
>
>
>
>   
>> I attached an image that shows parts of the corresponding parts of the
>> example file, the CV file, the schema file and the mapping file.
>>
>> Best,
>>   Marc
>>     
>
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