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

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Thanks for adding that, Lennart.  I like the idea of cvParams to
annotate what the software did to create the file.

One use case that we have is a conversion (say RAW -> mzML) by a single
program with various modules that may be turned on or off (centroiding,
peak picking, recalibration, precursor recalculation, etc.).  I think it
is very useful to record which of these modules was used during the
creation of the mzML file. 

Another thing from a maintainability perspective:  software will add
functionality as it grows, so I don't think it's a good idea to
pigeon-hole it via parenting in the CV.  It will be much more convenient
to add cvParam annotations for future versions of the software than to
request a CV change.  In fact, changing the CV parents may be valid for
a new version of a program, but then may be incorrect/misleading when an
old version is used.

Darren

-----Original Message-----
From: psi...@li...
[mailto:psi...@li...] On Behalf Of
Matthew Chambers
Sent: Thursday, February 14, 2008 8:15 AM
To: Mass spectrometry standard development
Subject: Re: [Psidev-ms-dev] mzML 0.99.9 SNAPSHOT software::type
attribute

I share your concern Lennart. AFAIK, Xcalibur is the name of a library 
or suite of applications, it's not a single program. It could be called 
once for instrument control (acquisition) and another time for peak 
picking & export to XML (currently only mzData). There may be other 
processing options in the future. It probably either needs more than one

entry in the CV (one per application in the Xcalibur suite) or we need a

separate group of CV terms to annotate software purpose. The former 
route would probably be more CV-friendly and intuitive. The latter route

would require all the semantic logic about which software CV terms are 
able to be used for which purpose to be in the validator or in client 
software, a bad idea IMO.

-Matt

Lennart Martens wrote:
> Hi Angel,
>
>
>   
>> I would have thought the ontology entry for XCalibur would have 
>> qualified it as acquisition software (e.g. this should have been
encoded 
>> into the CV element and hence referencing the accession MS:1000532
would 
>> suffice to identify it as acquisition software.)
>>     
>
> Seems like a very reasonable suggestion to me. Currently not
implemented 
> in the CV, but I'll make another tentative note on CV development.
>
> One thing that I just thought of: what if a piece of software can 
> perform multiple functions (i.e.: 'acquisition' as well as
'peakpicking' 
> -- doable in the CV through simple multi-parenting), but is used in
only 
> one capacity (say 'acquisition') while another piece of software is
used 
> for the other functionality (e.g., I used 'Mascot Distiller' for 
> 'peakpicking').
>
> Do we want to keep track of such things, and is this possibly an 
> argument against CV encoding here?
>
>
> Cheers,
>
> lnnrt.
>
>   
>> On Thu, Feb 14, 2008 at 6:21 AM, Lennart Martens 
>> <len...@eb... <mailto:len...@eb...>> wrote:
>>
>>     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
>>
<http://www.ebi.ac.uk/%7Elmartens/mzML/20080214_mzML0.99.9_SNAPSHOT.xsd>
>>
>>     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.
>>     
>
>
>
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