Re: [Psidev-pi-dev] AnalysisXML PMF Example

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

Hi David,

You may be right that the parameter should be optionally anyway, but in this
particular example is there not some score assigned to the peptide-spectrum
identification?

In the equivalent MS/MS example, we have:

            <pf:cvParam accession="PI:00171" name="mascot:score"
cvRef="PSI-PI" value="62.72" />
            <pf:cvParam accession="PI:00172" name="mascot:expectation value"
cvRef="PSI-PI" value="0.000863428353297988" />
            <pf:cvParam accession="PI:99999" name="mascot_rank"
cvRef="PSI-PI" value="1" />

Are the same sort of scores not valid for PMF as well...?

Cheers
Andy


> -----Original Message-----
> From: David Creasy [mailto:dc...@ma...]
> Sent: 16 October 2008 12:29
> To: psi...@li...
> Subject: [Psidev-pi-dev] AnalysisXML PMF Example
> 
> Hi All,
> 
> There's an example PMF file here:
> 
> http://code.google.com/p/psi-pi/source/browse/trunk/examples/PMF_example.axml
> 
> The only small problem that I can see is that for
>  <SpectrumIdentificationItem>
> 
> the schema has:
>   <xsd:element ref="psi-pi:PeptideEvidence" minOccurs="0"
> maxOccurs="unbounded"/>
>   <xsd:element ref="pf:Param" maxOccurs="unbounded"/>
> 
> and I can't think of any required CV here
> 
> To find it, search for
> <pf:cvParam accession="PI:xxxxx" name="TODO: Required content, but nowt
> to say here here"
> 
> I suggest that we have minOccurs=0 for pfParam here unless anyone disagrees?
> 
> David
> 
> --
> David Creasy
> Matrix Science
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