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

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

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

 

+ 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