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

[Fredrik L. <Fre...@im...>]

Isn't the actual usage of the software described under dataProcessing? 
If the same software suite was used for two processing steps it can be 
defined using two separate dataProcessing elements. I think what Angel 
proposes should work out fine. Ok, there may be some ambiguities s for 
converting mzML to mzXML if a piece of software belongs to several 
software types categories, but apart from that I see no problem. Maybe a 
CV term for 'data acquisition' could be added as a MS:1000543 ( data 
processing action), though? Or doesn't data acquisition qualify as 
'processing'?

Fredrik

Matthew Chambers skrev:
> 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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