Re: [Psidev-pi-dev] Ambiguous residues - CV

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

Looks fine to me, only minor consideration might be the "value" data type for:
Alternate single letter codes. You could imagine values getting encoded as "DN"
"D N" "D,N" or "[D/N]" etc.

Elsewhere in the AnalysisXML schema, we have defined an extension data type
listOfChars, which enforces that values are given as space separated chars: "D N
M", it would be nice to follow a similar convention although I don't know if it
would make sense to put this newly defined data type into the CV?

Cheers, Andy




> -----Original Message-----
> From: David Creasy [mailto:dc...@ma...]
> Sent: 24 November 2008 14:43
> To: psi...@li...
> Subject: [Psidev-pi-dev] Ambiguous residues - CV
> 
> Hi all,
> 
> We need CV for the <AmbiguousResidue> element in the analysisXML
> MassTable. This is when, for example, a search engine sees an 'X' in the
> fasta file and it tries every other defined residue mass. We decided
> that we wanted to use CV here in case a search engine implements complex
> rules for these ambiguous residues.
> 
> I propose 2 initial CV items to allow either mass or previously defined
> residue.  An example of each type shown in context below:
> 
> <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>
> 
> The "Alternate mass" item would be: unitAccession="UO:0000221"
> unitName="dalton".
> 
> Does this sound reasonable?
> 
> Cheers,
> 
> David
> 
> --
> David Creasy
> Matrix Science
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