Re: [Psidev-ms-dev] Current mapping file

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

Hi Lennart,

i'll inform you if i find other dangling ends in the mapping file.
i'm only 70% through with out mzML implementation.

Best,
  Marc

Lennart Martens wrote:
> Hi Marc,
>
>
>   
>> thanks for the up-to-date link.
>> The other version I found is at: 
>> http://psidev.cvs.sourceforge.net/psidev/psi/psi-ms/mzML/schema/ms-mapping.xml?view=log 
>>     
>
> Well spotted. I have now deleted this from CVS, and remarked in the log 
> comment of the commit that the files should be obtained from the psidev 
> SVN instead, along with the path to the validator configuration files.
>
>
>   
>> I have several questions/comments regarding the mapping file.
>>
>> Comment 1:
>> There is no mapping for the "/mzML/run" tag
>>     
>
> Correct, I couldn't easily find anything that we require or expect 
> there, so I let the rule out. Maybe there should be one or more rules 
> added for this location, but fleshing out the mapping file is still a 
> work in progress. You're very welcome to make suggestions, actually.
>
>
>   
>> Comment 2:
>> There is no mapping for the 
>> "/mzML/run/spectrumList/spectrum/spectrumDescription/precursorList/precursor/isolationWindow" 
>> tag
>>     
>
> Correct, we should add a meaningful rule here.
>
>
>   
>> Comment 3:
>> There is no mapping for the "data processing parameter" terms (MS:1000630)
>>     
>
> Correct again; needs to be added.
>
>
>   
>> Question 1:
>> According to the mapping file the "ms level" term (MS:1000511) should be 
>> under "spectrumDescription", but is under "spectrum" in the tiny1 example.
>> Which one is right?
>>     
>
> Good question. Can't remember off the top of my head what this should 
> be. So you can see: there's work yet to be done on the mapping file!
>
>
> Essentially, my main effort in these matters right now is spent on 
> getting our reference validator up and running. Once that is achieved, 
> the mapping file can be refined as we go along (the whole thing is 
> descriptively configured from the XML file, so no code needs changing).
>
> I think we should probably have a conference call dedicated to the 
> mapping file at a point in the near future, but that is open to discussion.
>
> Regardless, it would be good to have the reference validator out there 
> first, so people are free to play with the mapping rules and instance 
> documents. At the EBI, we're ironing out the last bugs in the validator 
> now (while the mzML validator itself is simple and consists of nearly 
> trivial code, this is only because (i) we have this rather complex but 
> minimal memory footprint jmzML component that effectively uses an mzML 
> file as a cache file, and (ii) we build the entire back-end on the 
> generic PSI validator framework, which is a very complicated suite of 
> modules that are high-tech codepieces in their own right -- this 
> framework is also used by the PSI-MI people, for instance).
>
>
> Cheers,
>
> lnnrt.
>
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