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

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Hi all,

It looks like I was wrong about the "choice" xsd concept. It only works 
on elements, not attributes. If we want to do this with schematic 
validation, we could make two acquisition types:
<acquisition spectrumRef="..." />
<externalAcquisition sourceFileRef="..." spectrumRef="..." 
nativeID="(optional)" />

Or we can keep the current suggestion and leave it to the semantic 
validator to enforce the right attributes:
spectrumRef (infer reference as current file and spectrumRef is IDREF 
pointing to an existing spectrum's id)
sourceFileRef + externalNativeID (original file is native)
sourceFileRef + externalSpectrumID (original file is mzML)

-Matt

Eric Deutsch wrote:
>
> Hi everyone, here are the minutes for the telecon. Please see action 
> items for you. Anyone not on the call willing to help out is welcome.
>
> Present: Darren, Matt, Eric, Jim, Pierre-Alain
>
> Thank you to Juan Antonio for setting up the call.
>
> Agenda:
>
> - What is the purpose of <mzML> id and accession attributes?
>
> + Make the id= attribute optional in schema
>
> + Recommend in the documentation that you use LSID or local identifiers
>
> + Make all sample instance documents use a psidev LSID
>
> + Leave accession= optional as is, perhaps with better documentation
>
> - Make <run> instrumentConfigurationRef optional or remove it:
>
> - if remove, then this attribute can be required in <scan>
>
> - if optional, semval must insure that it is provide either in <run> 
> or <scan>
>
> + OR consensus opinion: rename <run> instrumentConfigurationRef to 
> defaultInstrumentConfigurationRef and keep it required
>
> + Document the intrumentConfiguration a bit better. Applies to LTQ-FT 
> but not LTQ, for example. For different modes, use ParamGroups
>
> + Discussion of issue of how to use ParamGroups without having to do 
> two passes through the file.
>
> - Issue of exactly how other spectra are referenced in <acquisition>
>
> + We agree to move forward with Matt suggestion:
>
> spectrumRef (infer reference as current file and spectrumRef is IDREF
>
> pointing to an existing spectrum's id)
>
> sourceFileRef + externalNativeID (original file is native)
>
> sourceFileRef + externalSpectrumID (original file is mzML)
>
> For example external mzXML files, the externalNativeID would refer to 
> mzXML scanNumber
>
> In fact, anything that’s not mzML would have externNativeID
>
> Matt says that XML schema can enforce these various options
>
> - MIAPE spreadsheet?
>
> + Pierre-Alain has spreadsheet. Darren added some comments trying to 
> implement it
>
> + Rename Darren’s tiny2 to tiny5 or some other name since “tiny2” is 
> used by another document
>
> + Get miape-ms.pwiz.mzML posted
>
> + Pierre-Alain will continue to work on the spreadsheet
>
> + Before next call, send out or post miape-ms.pwiz.mzML and 
> spreadsheet of issues to discuss
>
> - CV?
>
> + Randy has pink teddy bear, but haven’t heard from him
>
> + Eric will take it and work on some changes to the CV
>
> + Eric will create the CV spreadsheets and start sending to vendors
>
> + Some contacts: Bruker :Herbert Thiele? Waters: Ronan O’Malley?
>
> - documentation?
>
> + latest is posted without figures
>
> - schema?
>
> + Eric will add Darren & Matt as a developers (dkessner) (chambm)
>
> + Darren will update 0.99.10 to 0.99.11 with changes above
>
> + Matt can help with multiple accession configs in <acquisition>
>
> - website
>
> + Eric post 0.99.10 schemas
>
> + Darren verify that tiny.pwiz encodes all ideas of tiny1 and then 
> post as a single tiny1
>
> - example files
>
> + Jim has an example that he will send out
>
> + Jim will send out examples of the nativeIDs for Thermo
>
> ------------------------------------------------------------------------
>
> *From:* Eric Deutsch
> *Sent:* Monday, May 05, 2008 12:12 AM
> *To:* 'Mass spectrometry standard development'; Juan Antonio Vizcaíno 
> González
> *Cc:* Eric Deutsch
> *Subject:* RE: PSI-MSS WG call Tuesday
>
> Hi everyone, as previously mentioned, the PSI Mass Spectrometry 
> Standards Working Group call is Tuesday May 6 at 9am PDT:
>
> http://www.timeanddate.com/worldclock/fixedtime.html?day=6&month=5&year=2008&hour=17&min=0&sec=0&p1=136 
> <http://www.timeanddate.com/worldclock/fixedtime.html?day=6&month=5&year=2008&hour=17&min=0&sec=0&p1=136>
>
> + Germany: 08001012079
>
> + Switzerland: 0800000860
>
> + UK: 08081095644
>
> + USA: 1-866-314-3683
>
> + Generic international: +44 2083222500 (UK number)
>
> access code: 297427
>
> The agenda will be to review and discuss what remains to be done to 
> finish up mzML, including the latest release and some recent issues 
> discovered while making examples.
>
> Thanks,
>
> Eric
>
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