Re: [Psidev-pi-dev] PSI-PI Working group conference call on Wednesday 26th November at 4:00pm UK time

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

Hi Andy

Jones, Andy wrote:
> I have a query about something in the minutes:
> 
> <MassTable is="MT1">
>  <Residue Code="A" Mass="71.037114"/>
>  ...
>  <Residue Code="Y" Mass="163.063329"/>
> 
>  <AmbiguousResidue Code="B">
>    <pf:cvParam accession="PI:xxxx" name="Alternate single letter codes"
> cvRef="PSI-PI" value="DN"/>
>  </AmbiguousResidue>
>  <AmbiguousResidue Code="Z">
>    <pf:cvParam accession="PI:yyyy" name="Alternate mass" cvRef="PSI-PI"
> value="129.042593"/>
>    <pf:cvParam accession="PI:yyyy" name="Alternate mass" cvRef="PSI-PI"
> value="128.058578"/>
>  </AmbiguousResidue>
>  . . .
> </MassTable>
> 
> 
> I think we agreed that the value attribute above for "Alternate single letter
> codes" should be "D N" i.e. space separated chars, is this correct?
Yes, this is what we agreed.

> 
> If so, I'm not sure if I was supposed to add this as documentation to the XSD or
> if we want to add this documentation to the CV term (the latter seems better to
> me).
Adding it to the CV term seems better. However, Martin proposed a 
different approach in an email a little earlier today:


 > What do you think about:?
...
    <AmbiguousResidue Code="B" ResidueRef="D N"/>
    <AmbiguousResidue Code="Z">
      <pf:cvParam accession="PI:yyyy" name="Alternate mass" cvRef="PSI-PI"
  value="129.042593"/>
      <pf:cvParam accession="PI:yyyy" name="Alternate mass" cvRef="PSI-PI"
  value="128.058578"/>
    </AmbiguousResidue>

ResidueRef can be type listOfChar.

Disadvantage is the mix of schema and CVParam mechanisms...
------------------

I don't have a preference either way. Any thoughts Andy?

David

> 
> Cheers, Andy
> 
> 
> 
>> -----Original Message-----
>> From: David Creasy [mailto:dc...@ma...]
>> Sent: 27 November 2008 13:35
>> To: psi...@li...
>> Subject: Re: [Psidev-pi-dev] PSI-PI Working group conference call on Wednesday
>> 26th November at 4:00pm UK time
>>
>> Minutes are here:
>>
>> http://psidev.info/index.php?q=node/395
>>
>> Most action items already done...
>>
>>
>>
>> David Creasy wrote:
>>> Hi everyone,
>>>
>>> There will be an AnalysisXML working group conference call on WEDNESDAY
>>> (instead of Thursday, because it is Thanksgiving in the US) at:
>>>
>> http://www.timeanddate.com/worldclock/fixedtime.html?day=26&month=11&year=2
>> 008&hour=16&min=0&sec=0&p1=136
>>>
>>> Minutes, including action items ;) from last meeting at:
>>> http://psidev.info/index.php?q=node/392
>>>
>>> Agenda:
>>> 1. Review of minutes of last meeting
>>>
>>> 2. Internal fragment ions
>>>
>>> 3. Ambiguous residues
>>>
>>> 4. Status of mapping document, CV and examples.
>>>
>>> 5. Please review the latest documentation:
>>>
>>> http://psi-
>> pi.googlecode.com/svn/trunk/specification_document/analysisXML_SpecificationDr
>> aft.doc
>>>
>>>
>>> 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
>> Matrix Science
>> 64 Baker Street
>> London W1U 7GB, UK
>> Tel: +44 (0)20 7486 1050
>> Fax: +44 (0)20 7224 1344
>>
>> dc...@ma...
>> http://www.matrixscience.com
>>
>> Matrix Science Ltd. is registered in England and Wales
>> Company number 3533898
>>
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-- 
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344

dc...@ma...
http://www.matrixscience.com

Matrix Science Ltd. is registered in England and Wales
Company number 3533898