Re: [Psidev-ms-dev] [HUPO-PSI/psi-ms-CV] Alternating polarity missing (#7)

[mayerg97 <ger...@ru...>]

Hello Steffen,

would it make sense to make 'alternating polarity scan' a child of 'run 
attribute'?

[Term]
id: MS:1002826
name: alternating polarity mode
def: "Polarities of the scans of a run are alternating, i.e. both 
positive and negative mode scans are acquired." [PSI:MS]
is_a: MS:1000857 ! run attribute

Cheers,
Gerhard


Am 24.08.2017 um 00:16 schrieb sneumann:
>
> Hi, the reason I brought this up was because ISA-Tab is describing the 
> content of an mzML file, i.e. an attribute of the |<run>| as such 
> being positive/negative/alternating.
> As indicated in my first comment, "alternating" can't be a scan 
> attribute, but when I searched our obo for "alternating" that parent 
> term came up. Maybe that was the reason why alternating was obsoleted:
> https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo#L3241
> So a better home for "alternating polarity" could be "MS:1001954 
> acquisition parameter" (which currently has no children at all ?!) and 
> which resides below the |<scanSettings>| of the mzML,
> which I think is the closest to describing the instrument method we 
> can find in mzML.
> The mapping file currently does not specify which CV terms can go 
> below |<scanSettings>|.
> I also realised we had obsoleted "ionization mode" 
> https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo#L111 , 
> which probably sounded a bad idea as scan attribute, but which might 
> have been good to keep among the |<scanSettings>|.
>
> So what about:
>
>  1. Grammar fix, plus removal of mentioning alternating as scan attribute:
>
> |[Term] id: MS:1000465 name: scan polarity def: "An acquisition mode to 
> which specifies whether polarity is negative or positive." [PSI:MS] 
> relationship: part_of MS:1000441 ! scan |
>
>  2. still add "alternating", but with different parent than proposed
>     above:
>
> |[Term] id: MS:1000XXX name: alternating polarity mode def: "Polarity 
> of the scans is alternating, i.e. both positive and negative mode 
> scans are acquired.[PSI:MS] is_a: MS:1000009 ! ionization mode |
>
>  3. Consider re-adding MS:1000009 ! ionization mode, but now as
>     acquisition parameter (not sure what it was before):
>
> |[Term] id: MS:1000009 name: ionization mode def: "Whether positive or 
> negative ions are selected for analysis by the spectrometer." [PSI:MS] 
> is_a: MS:1001954 ! acquisition parameter |
>
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*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

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