Re: [Psidev-ms-dev] indexedmzML: scanNumber / acquisition number

[Kessner, D. E. <Dar...@cs...>]

I'd vote for idNative or nativeID, since "scan" may not always apply.

Darren


-----Original Message-----
From: psi...@li...
[mailto:psi...@li...] On Behalf Of Joshua
Tasman
Sent: Monday, February 25, 2008 12:54 PM
To: Mass spectrometry standard development
Subject: Re: [Psidev-ms-dev] indexedmzML: scanNumber / acquisition
number

Good thinking.  As long as all parser authors (me, you and Matt?) are on
board with this, this seems like a good pragmatic solution (and I assume
Matt is, since he first proposed the "cooridinate string" idea).

(And, I'd suggest renaming "externalID" to "nativeScanID", or something
similar, to be more specific.)

Josh


Kessner, Darren E. wrote:
> Sorry -- that didn't make sense.  This is more what I had in mind:
> 
> <index>
>    <externalIDTypeList count="2">
>       <cvParam .../>
>       <cvParam .../>
>    </externalIDTypeList>
>    ...
>    <offset id="S19" externalID="(19,123)">4826</offset>
>    ...
> </index>
> 
> 
> Darren
> 
> 
> -----Original Message-----
> From: psi...@li...
> [mailto:psi...@li...] On Behalf Of
Joshua
> Tasman
> Sent: Monday, February 25, 2008 12:41 PM
> To: Mass spectrometry standard development
> Subject: Re: [Psidev-ms-dev] indexedmzML: scanNumber / acquisition
> number
> 
> Thanks, Darren.  Your version would work for Thermo, but not for other
> vendor schemes that doesn't have a flat scalar index for denoting
scans.
> Others have various "coordinate systems" to determine each scan, such
as
> requiring 'cycle', 'period', 'method', 'scan' (off the top of my head,
> maybe slightly different) so you'd need something like
> 'externalIDTypeAccession1', 'externalIDTypeAccession2',
> 'externalIDTypeAccession3'...
> 
> Ah-- but my "fixed attributes" propose requires an indexedmzXML schema
> rev when a new coordinate system is introduced.  Can anyone out there
> think of a way to flexibly use varying numbers of accessions without
> taking up too much space at the index?  I'm back to thinking you'd
need
> a "nativeScanRef" subelement with unbounded number of cvParams, but
this
> would be pretty big.  Maybe that's just what's needed for this.
> 
> Josh
> 
> Kessner, Darren E. wrote:
>> I'm fine with that, Josh.
>>
>> Here's another idea, to make use of the existing vocabulary terms:
>>
>> <index>
>>
>>   <offset id="S19" externalID="19"
> externalIDTypeAccession="MS:1000532"
>> externalIDTypeName="Xcalibur" >4826</offset>
>>
>> ...
>>
>> </index>
>>
>>
>> Darren
>>
>>
>>
>> -----Original Message-----
>> From: psi...@li...
>> [mailto:psi...@li...] On Behalf Of
> Joshua
>> Tasman
>> Sent: Monday, February 25, 2008 12:21 PM
>> To: Mass spectrometry standard development
>> Subject: Re: [Psidev-ms-dev] indexedmzML: scanNumber / acquisition
>> number
>>
>> Darren and Matt:
>>
>> Thinking about it-- why not just have a slew of optional named
>> attributes for the <index>, like: "XcaliburNum", "MassLynxCycle",
>> "MassLynxPeriod", 
>> "AnalystCycle", etc.?  Less elegant, but should do the trick for fast
>> index parsing, and make me happy by avoiding a convention-based
string
>> for each vendor and keeping it human readable?  I'd propose that if,
> in
>> a specific file, these are used in the index, they should be
> enumerated
>> more fully in the <spectrum> with cvParams, as previously suggested.
>>
>> Josh
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