[Psidev-ms-dev] mzML 0.99.9 SNAPSHOT software::type attribute

[Lennart M. <len...@eb...>]

Hi Darren, hi PSI-MS enthousiasts,


I have included the ability to use cvParams in the 'software' element in 
a new schema iteration as per your suggestion.
Find it here:

http://www.ebi.ac.uk/~lmartens/mzML/20080214_mzML0.99.9_SNAPSHOT.xsd


I have also included an example instance document that is valid against 
this schema (do note that it currently uses a made-up CV term for the 
software type). Note that this example instance also has the binary 
array thingie at software level, and is essentially a hack of tiny1.
Find it here:

http://www.ebi.ac.uk/~lmartens/mzML/20080214_example_mzML0.99.9_SNAPSHOT.mzML

Sorry for the convoluted filenames, but it'll help keep things clear and 
separated, and somewhat archived.

One more note: if we get a consensus for this approach, we should 
probably extend the CV as well, so I'm already making a note about 
potentially including software types in a dedicated branch in the CV -- 
tentatively, of course.


Cheers,

lnnrt.

Kessner, Darren E. wrote:
> Hi all,
> 
>  
> 
> Please excuse me if this has been discussed before. 
> 
>  
> 
> In mzXML, the <software> element is encoded as follows:
> 
>     <software type="acquisition"
> 
>                    name="Xcalibur"
> 
>                    version="1.3 alpha 8"/>
> 
>  
> 
> In mzML, we have:
> 
>     <software id="Xcalibur">
> 
>         <softwareParam cvLabel="MS" accession="MS:1000532" 
> name="Xcalibur" version="2.0.5"/>
> 
>     </software>
> 
>  
> 
> Note that the name and version are encodable, but there is no convenient 
> place to save the "type" attribute, since the <software> element does 
> not have <cvParam> or <userParam> sub-elements.
> 
>  
> 
> Currently this causes a loss of this info when converting mzXML->mzML. 
> 
>  
> 
> If there is a good place to put this attribute, the conversion mzXML -> 
> mzML -> mzXML will be doable with no loss of information.  (I think this 
> is the last missing piece).  Or perhaps it's no great loss?  I don't 
> have a strong attachment to this attribute -- just thought it would be 
> nice to be able to get the same mzXML after converting to and from mzML...
> 
>  
> 
> Thoughts?
> 
>  
> 
>  
> 
> 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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