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

[Pierre-Alain B. <pie...@is...>]

Hi,

David Creasy wrote:
> 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).
you can find a temp version at 
ftp://ftp.genebio.com/div/MIAPE-mzML-mapping.01.xls   
>
>>
>> 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 ;)
the files used to generate the AnalysisXML file...
>
>>
>> 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
voila,
Pierre-Alain
>>
>>
>> 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
>>>>
>>>>     
>>>
>>>   
>