[Psidev-ms-dev] scanNumber not in <scan> (was: Re: Teleconference Tuesday 19 Feb 2008)

[Eric D. <ede...@sy...>]

Hi Randy, regarding:

> Also, I haven't heard back about the relationship between the
'scanNumber'
> attributes and the scan elements.  Has anyone looked at this yet?
> Can we also discuss how this is supposed to work tomorrow?

scanNumber in the <spectrum> element is perhaps somewhat misplaced. It
does belong in <scan>, yes. BUT, since the scan number has historically
been an important handle for identifying the spectrum and for use in the
mzXML indexing scheme, it has been promoted to the top.

<spectrum id="S19" scanNumber="19" msLevel="1">
	<cvParam cvLabel="MS" accession="MS:1000580" name="MSn spectrum"
value=""/>
	<spectrumDescription>
		<scan instrumentRef="LCQ Deca" ???scanNumber="19"???>

If we move it into <scan>, this may be more semantically correct, but it
will almost surely make the parser software writers jobs more difficult.
This may be a case of function over beauty.

This is somewhat mitigated by the fact that we now have an id attribute.

I'm not inclined to change it because I'm lazy and because I suspect it
will make Darren and Brian sad.

But we can discuss.

If we allow the previous chromatograms in <spectrum> we then may be
faced with generating bogus scan numbers to keep the validator happy. If
it's in scan, and there is no scan, that's less of a problem.

If we move scanNumber into <scan>, what's to prevent msLevel following
suit?

http://blog.b92.net/arhiva/files/images/can%20of%20worms.jpg

Eric





> -----Original Message-----
> From: psi...@li...
[mailto:psidev-ms-dev-
> bo...@li...] On Behalf Of Randy Julian
> Sent: Monday, February 18, 2008 10:22 AM
> To: Mass spectrometry standard development
> Subject: Re: [Psidev-ms-dev] Teleconference Tuesday 19 Feb 2008
> 
> I'd like to get a couple of schema items on the agenda tomorrow.
> 
> I've been asking about a possible change in the schema regarding
> msLevel.  As an alternative to moving the attribute, or making it
> optional, I would like to propose that we allow non-MS channels
acquired
> by the MS data system and stored in the raw file to be marked as
> msLevel=0.  This would require a change to the specification document
> but would allow software to ignore non-spectral content (whatever it
> might be) if the level is not at least 1.
> 
> Another approach which is also consistent with the rest of the schema
is
> to make the attribute a cvParam like the axis names.  This would
require
> a schema change and shift the validation of msLevel to the validator
> program.  If there is strong support for a required msLevel attribute
in
> the current location, we could still represent the other signals with
> the suggestion above.
> 
> Also, I haven't heard back about the relationship between the 'scan'
> number attributes and the scan elements.  Has anyone looked at this
yet?
> Can we also discuss how this is supposed to work tomorrow?
> 
> Thanks,
> Randy
> 
> 
> -----Original Message-----
> From: psi...@li...
> [mailto:psi...@li...] On Behalf Of
> Lennart Martens
> Sent: Monday, February 18, 2008 1:07 PM
> To: Mass spectrometry standard development
> Subject: [Psidev-ms-dev] Teleconference Tuesday 19 Feb 2008
> 
> Dear PSI-MS Enthousiasts,
> 
> 
> The next telephone conference for the PSI-MS development group will
take
> 
> place on Tuesday, 19 february 2008.
> 
> The phone conference will take place at the time indicated below
(please
> 
> find a location near you ):
> 
>
http://www.timeanddate.com/worldclock/fixedtime.html?day=19&month=2&year
> =2008&hour=17&min=0&sec=0&p1=0
> 
> phone numbers are:
> 
> + Germany: 08001012079
> 
> + Switzerland: 0800000860
> 
> + UK: 08081095644
> 
> + USA: 1-866-314-3683
> 
> + Generic international: +44 2083222500 (UK number)
> 
> access code: 297427
> 
> 
> You can also view these details online on the PSI website:
> 
> http://www.psidev.info/index.php?q=node/313
> 
> 
> Best regards,
> 
> lnnrt.
> 
>
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