Re: [Psidev-ms-dev] PSI-MSS WG Tuesday call reminder

[Angel P. <an...@ma...>]

Hi Steve, Is your question whether we can successfully round-trip the
numbers? Eg. go from an ascii format to mzML back to originating ascii
format and get the same exact numbers? I believe that when we pack the
numbers and unpack them (at least in my non-validating ruby implementations)
the numbers and significance are completely the same. E.g. 1.005 === 1.005
and not 1.005000000000001

-angel

On Thu, Jun 11, 2009 at 11:33 AM, Stein, Stephen E. Dr. <
ste...@ni...> wrote:

>  Congrats on a new version…..
>
>
>
> However, I wanted to again state what I think is a defect in the standard –
> the inability to accept an ASCII peak list. This prevents us from using mzML
> it as the format for libraries or reference data.
>
>
>
> --- 1 is different than 1.0 and different than 1.00 ….
>
>
>
> this difference, to some, is non trivial and changes the meaning of
> reference data when converted to binary.
>
>
>
> Also, the ability to see read the data is nice for those who want to do it.
>
>
>
> I suppose it’s addition will do too much damage to add to 1.2 – but I just
> felt that I should bring it up again as our needs have not changed.
>
>
>
> -Steve Stein
>
>
>  ------------------------------
>
> *From:* Eric Deutsch [mailto:ede...@sy...]
> *Sent:* Tuesday, June 09, 2009 12:02 PM
>
> *To:* 'Mass spectrometry standard development'
> *Cc:* 'Eric Deutsch'
> *Subject:* Re: [Psidev-ms-dev] PSI-MSS WG Tuesday call reminder
>
>
>
> Present: Marc, Jim, Matt, Eric, Lennart, Pierre-Alain
>
>
>
> 1) mzML 1.1.0
>
> - Released!
>
> + The whitespace issue in the xsd resolved before
>
> - Allowed binarydata data types
>
> + Add back in 32- and 64-bit integer. Those terms should be unobsoleted.
> There were there
>
> + Add string array: null-terminated array of strings. Must have as many
> nulls as elements.
>
> + Matt will add these to the CV
>
> + It will be implemented somehow in ProteoWizard and OpenMS
>
> + Matt will added another CV type which is binarydatatype and then
> annotated mzArray, IntensityArray, and chargeArray with the appropriate
> types
>
> - ASMS
>
> + There is a group that just put together a “unified” format for ion
> mobility mass spec. Matt and Eric met him, and we will followup
>
> + Also had discussion with ANiML. Being done through ASTM
>
> - ASMS might help out with CV
>
> + David Sparkman may help us out.
>
> + Eric will update MSS WG page
>
> + Eric will email Juan Antonio about top page
>
> + Marc will double check with Andreas Römpp on units addition and then add
> them as is
>
>
>
> 2) TraML development
>
> - Feedback from ASMS
>
> - Implementations
>
> + ProteoWizard has some implementation. OpenMS does as well by Andreas. Jim
> is working on something
>
> - cvParams vs attributes
>
> + Problem with attributes is lack on units specification
>
> + Problem with attributes is default value ambiguity in C++
>
> + change transition name to id of type xsd:string
>
> + Apply rule: any attribute that is not an id or a Ref should be switched
> to cvParam
>
> + How does mzIdentML handle b9-18^2 ? Try to do he same?
>
> + What about string values?
>
> + Matt is advocating more cvParams, Pierre-Alain as well. Jim as well.
>
> + Make normalizationStandard should be cvParams H-PINS
>
> + Eric will make another rev beased on this.
>
>
>
> + Meet again next week same time
>
>
>
>
>   ------------------------------
>
> *From:* Eric Deutsch [mailto:ede...@sy...]
> *Sent:* Monday, June 08, 2009 3:41 PM
> *To:* 'Mass spectrometry standard development'
> *Cc:* 'Eric Deutsch'
> *Subject:* PSI-MSS WG Tuesday call reminder
>
>
>
> Hi everyone, the next PSI Mass Spectrometry Standards Working Group call
> will be Tuesday 8am PDT:
>
>
>
>
> http://www.timeanddate.com/worldclock/fixedtime.html?day=09&month=6&year=2009&hour=16&min=0&sec=0&p1=136
>
>
>
> 08:00 San Francisco
>
> 11:00 New York
>
> 16:00 London
>
> 17:00 Geneva
>
>
>
> + Germany: 08001012079
>
> + Switzerland: 0800000860
>
> + UK: 08081095644
>
> + USA: 1-866-314-3683
>
> Generic international: +44 2083222500 (UK number)
>
>
>
> access code: 297427
>
>
>
> Agenda:
>
>
>
> 1) mzML 1.1.0
>
> - Released!
>
> - Allowed binarydata data types
>
> -
>
>
>
> 2) TraML development
>
> - Feedback from ASMS
>
> - Implementations
>
> - cvParams vs attributes
>
>
>
>
>
>
>
>
>
>
>
>
>
>
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>


-- 
Angel Pizarro
Director, ITMAT Bioinformatics Facility
806 Biological Research Building
421 Curie Blvd.
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215-573-3736