Re: [Psidev-ms-dev] mzML's binary arrays

[sneumann <sne...@ip...>]

Moin!

Sehe ich das richtig, dass der FeatureFinder
demnächst neben FeatureXML auch mzML ausspuckt ?

Gruss,
Steffen

On Mi, 2008-06-25 at 09:16 +0200, Marc Sturm wrote:
> Hi Eric,
> 
> i agree that less custom encoding is desirable to make files exchangable
> between different tools. However in this case i would go both ways,
> depending on the significance of the term.
> 
> (1)
> I use these arrays to store debug information of an algorithm and add
> quite a few arrays, depending on the charge states i look at:
> 
> pattern_score_1
> pattern_score_2
> pattern_score_... (one per charge)
> intensity_score
> local_maximum
> trace_score
> 
> Putting the name in the userParam is not a good idea because it makes
> these arrays unusable for other tools - too custom in my opinion.
> Adding a CV term for each such debug variable would however be too much.
> So i think the intermediate way is just right:
> Terms which are not generally usable should be put to a 'named custom
> array'. This would correpond to an optional XML attribute 'name' for the
> 'binaryDataArray' tag.
> But we have to state clearly in the documentation that for more general
> terms, a CV entry should be added.
> 
> (2)
> After peak picking we store much more information than the position and
> intensity. The arrays there are:
> 
> SignalToNoise
> fwhm
> leftWidth
> rightWidth
> maximumIntensity
> peakShape
> rValue
> 
> 'SignalToNoise' is alread a CV term. 'fwhm' would be a good candidate
> for a CV term as well.
> The rest is more algorihtm-dependent and no general concept which is why
> we could simply store them in a 'named custom array'.
> 
> What do you think?
> 
> Best,
> Marc
> 
> > Hi Marc, I think we would be better off creating CV terms for all the
> > kinds of arrays people want to encode. So I'm much rather get a request
> > that someone's software wants to write out "full width at half maximum"
> > and create a term, furnish an accession number, and thereby publicly let
> > all writer and reader authors know that this is a legal entity that
> > could occur. No schema change is necessary.
> >
> > I find this preferable to having a vague slot that could be filled with
> >
> > full width at half maximum
> > full width at half max
> > FWHM
> >
> > in an uncontrolled and variable way.
> >
> > This is our general aim for mzML. We would like to steer away from
> > custom ways of encoding data as much as possible.
> >
> > Does that seem reasonable?
> >
> > Would you like "full width at half maximum" to be added to the CV?
> 
> 
> 
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IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
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