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

[Jones, A. <And...@li...>]

Ah I missed this proposal. Are these are the only two mechanisms we need/want?
If so, we could just build the whole thing into the schema:

    <AmbiguousResidue Code="B" SubstituteResidues="D N"/>
   

   <AmbiguousResidue Code="Z">
      <AlternateResidue Mass="129.042593"/>
      <AlternateResidue Mass="128.058578"/>
    </AmbiguousResidue>

The downsides are if someone decides another mechanism is needed we cannot
extend this. Also, I'm not sure we can validate that only one mechanism or the
other is used (but this issue is the same whichever way we solve the problem).

In fact, do we need to allow it to be done both ways... Couldn't we just enforce
that it is done in the latter way, 

Cheers
Andy






> -----Original Message-----
> From: David Creasy [mailto:dc...@ma...]
> Sent: 27 November 2008 15:58
> To: Jones, Andy
> Cc: psi...@li...
> Subject: Re: [Psidev-pi-dev] PSI-PI Working group conference call on Wednesday
> 26th November at 4:00pm UK time
> 
> 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
> 
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
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