Re: [Psidev-pi-dev] PSI-PI Working group conference call on Wednesday 12th November at 4:00pm UK time

[David C. <dc...@ma...>]

Hi Pierre-Alain,

Pierre-Alain Binz wrote:
> Thanks David.
> FYI, for mzML, we had generated a excel mapping spreadsheet (if you want 
> to see it...)
Yes please. (I can't see it on psidev.info).

> 
> The format is ok for me. About the notes: the descriptions of what 
> should be the content from a MIAPE point of view are in the MIAPE 
> document, in the Annex table.
Oh yes...

> 
> Note also that for mzML-MIAPE MS mapping, there were a few items not 
> covered by MIAPE, and also not covered by mzML. The latest have either 
> been annotated for a future version of mzML (similar to the quantitation 
> in AnalysisXML), or just left out and annotated as such (for instance 
> flow rates, detector sensitivity). Either they are independant or an 
> estimation that looks more like an interpretation. We there need to 
> decide whether those should be taken out of MIAPE or not.
We will aim to add anything missing (apart from quantitation) before 
submission to the document process.

> 
> I have commented two of the notes. If there are unclear items, just put 
> a note in and I can clarify
Yes please! I can't remember what we intended from "Location of the 
files generated". The definition is:
"The location of the data generated. If made available in a public 
repository, describe the URI (for instance an url, or the url of the 
repository and the information on how to retrieve the data). If not made 
available for public access, describe the contact person reference or 
source and the internal coordinates of the data."

But _what_ data does this refer to? The peak list, the analysisXML 
document, intermediate files like Sequest .out files or any/all of 
these? If it's the analysisXML file, you presumably have it and you must 
know where you got it from ;)

> 
> One more: for mzML, we have two (at least) levels of stringency for the 
> validators: basic semantic and MIAPE compliance. Therefore we can deal 
> with legacy being compliant woth the format, even if it does not comply 
> with MIAPE
Sounds good,

David
> 
> 
> Cheers
> Pierre-Alain
> 
> David Creasy wrote:
>> I've started on the MIAPE conformance doc:
>>
>> http://psidev.info/index.php?q=node/386
>>
>> Can we discuss whether this is a suitable format on the call later.
>> (Looks as though we may have a couple of things to add to the schema...)
>>
>> Thanks,
>> David
>>
>> David Creasy wrote:
>>   
>>> Hi everyone,
>>>
>>> There will be an AnalysisXML working group conference call on WEDNESDAY
>>> (instead of Thursday) at:
>>> http://www.timeanddate.com/worldclock/fixedtime.html?day=12&month=11&year=2008&hour=16&min=0&sec=0&p1=136 
>>>
>>>
>>> Minutes from last meeting at:
>>> http://psidev.info/index.php?q=node/384
>>>
>>>
>>> Agenda: (strangely identical to last week, although progress has been 
>>> made!)
>>> 1. Review of minutes of last meeting
>>>
>>> 2. Status of mapping document and CV
>>>
>>> 3. Issue 30: Enzymes
>>>    http://code.google.com/p/psi-pi/issues/detail?id=30
>>>    Almost complete now?
>>>    http://code.google.com/p/psi-pi/issues/detail?id=30&can=1#c37
>>>
>>> 4. Other items on the issues list:
>>>    http://code.google.com/p/psi-pi/issues/list
>>>
>>> Dial in details:
>>>
>>> + Germany: 08001012079
>>> + Switzerland: 0800000860
>>> + UK: 08081095644
>>> + USA: 1-866-314-3683
>>> + Generic international: +44 2083222500 (UK number)
>>>
>>> access code: 297427
>>>
>>>     
>>
>>   

-- 
David Creasy
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