Re: [Psidev-pi-dev] CV term "scoring model"

[Pierre-Alain B. <pie...@is...>]

I'm fine with only one term.
In Phenyx, the GUI description in two levels is pointing to one file for 
each combination. The important information is the scoring model xml 
file itself (esquire3000-gbaa-is-hmm.scoring.xml for instance). The 
items in the GUI are "only" descriptors to help choosing the appropriate 
scoring file.
As the GUI information is always interpreted, we should just define if 
the instrument details corresponds to the GUI selection or to the 
effective "scoring model used".


FYI, the two levels "instrument type" and "scoring model" are 
represented in Phenyx in this "hyerarchical" manner for different reasons.
- One is to show the possibility to generate multiple specific scoring 
models for an instrument type (LTQ and Qtrap do not fragment in the same 
way) or to differentiate fragmentation pattern interpretation between 
say unmodified and systematically modified peptides (such as iTRAQ for 
instance)
- An other one is to avoid the one-long-list drop-dowm menu
- A third one is to explicitely describe different instrumental setups 
but using the same scoring model (ESI-Linear trap LTQ is the same 
scoring model as ESI-LTQ-Orbitrap CID_LTQ_scan_LTQ). Some people have 
difficulty to choose an ESI-trap scoring if they use an Orbitrap. Some 
users do not understand the difference between a fragmentation in the 
LTQ or the C-trap and need to be "guided" through the interface.
- And a fourth one is to allow each one to define its own "relationship"



Martin Eisenacher wrote:
> Hi Pierre-Alain!
>
> In the AnalysisXML CV we have a branch 
> "instrument details" with a sub-branch "instrument type" (e.g. ESI-QUAD, MALDI-TOF) and a 
> sub-branch "scoring model" which was probably created with phenyx in mind.
>
> What do you think: 
> Leave it as ONE term and specify a (string) value which is the name of the
> scoring model xml file in phenyx?
>
> Or specify (additionally) child terms for "default" scorings:?
> For example:
> esquire3000+.Da_.1.scoring.xml
> esquire3000+.Da_.2.scoring.xml
> esquire3000-gbaa-is-hmm.scoring.xml
> ...
> Some more?
>
>   bye from Bochum
>    Martin
>
>
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