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

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Hi,

Jones, Andy wrote:
> Ah I missed this proposal. Are these are the only two mechanisms we need/want?
One day, someone may well want to do something more involved...

> 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, 
Could do, but not so nice because:
  - It would be quite verbose - most search engines will use 'X' to mean
    all other residues.
  - It's a little harder to understand with just numbers.
    <SequenceCollection>
      <DBSequence id="A">
        <seq>MAXXPAVK...
      <Peptide
        <peptideSequence>MAKAPAVK
    ...
    <PeptideEvidence start="1" end="8" DBSequence_Ref="A" .....

Maybe safest to stick with the original proposal of just CV and accept 
that the list of chars is not properly validated?

David
> 
> 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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>>>> _______________________________________________
>>>> Psidev-pi-dev mailing list
>>>> Psi...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
>> --
>> 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
>> Build the coolest Linux based applications with Moblin SDK & win great prizes
>> Grand prize is a trip for two to an Open Source event anywhere in the world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> Psidev-pi-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev

-- 
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

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

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