Re: [Psidev-pi-dev] FW: Spec doc

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

Hi Andreas,

 > (Maybe the CV and mapping file look much clearer with enough absolut)
I'm not sure why you can see double
CV entries for the fragment and parent tolerance ;)

So, originally we had:
<PlusValue   >
<MinusValue  >

Andy suggested:
Andreas can you add: “search tolerance plus value” and “search tolerance 
minus value” to the CV and mapping file and I’ll change the schema, does 
this seem reasonable to everyone…?

I looked in the mapping file and saw:
         <CvMappingRule id="R17a" 
cvElementPath="/psi-pi:AnalysisXML/psi-pi:AnalysisProtocolCollection/psi-pi:SpectrumIdentificationProtocol/psi-pi:ParentTolerance/pf:cvParam/@accession" 
requirementLevel="MUST"  scopePath="" cvTermsCombinationLogic="OR">
             <CvTerm termAccession="PI:00402" useTermName="false" 
useTerm="false" termName="mass units" isRepeatable="false" 
allowChildren="true" cvIdentifierRef="PSI-PI" />
         </CvMappingRule>


and then must have forgotten what we were trying to do....

So, I think that we must add the two CV terms Andy originally suggested?
Could you do that please? (I don't think Martin will be doing any edits).

Thanks,

David

Andreas Bertsch wrote:
> Hi David,
> 
>>  I've updated the Mascot_MSMS_example.axml,
>>        <FragmentTolerance>
>>          <pf:cvParam accession="PI:00404" name="absolut mass unit"
>> value="0.5" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="dalton"
>> unitCvRef="UO" /> <pf:cvParam accession="PI:00404" name="absolut mass unit"
>> value="0.5" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="dalton"
>> unitCvRef="UO" /> </FragmentTolerance>
>>        <ParentTolerance>
>>          <pf:cvParam accession="PI:00403" name="relative mass unit"
>> value="0.1" cvRef="PSI-PI" unitAccession="UO:0000187" unitName="percent"
>> unitCvRef="UO" /> <pf:cvParam accession="PI:00403" name="relative mass
>> unit" value="0.1" cvRef="PSI-PI" unitAccession="UO:0000187"
>> unitName="percent" unitCvRef="UO" /> </ParentTolerance>
> Is there a reason to repeat the unit lines? I've added term UO:0000187 percent 
> to the allowed ones, this is a synonym of parts per hundred, however 
> separately listed in unit.obo...
> 
>>  but this doesn't validate:
> The file still does not validate with some new errors, as you suggested ;)
> Error: Name of CVTerm not correct: 'PI:00404 - absolut mass unit' should be 
> 'absolute mass unit'
> Error: Violated mapping rule 'R17a' number of term repeats at element 
> '/AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/ParentTolerance'
> Error: Violated mapping rule 'R17b' number of term repeats at element 
> '/AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/FragmentTolerance'
> 
> Blame me, if you experience other unexpected results.
> 
>>  I'm also slightly concerned about PSI-PI group getting the wrong(?)
>> reputation. Martin, could you change PI:00404 from being a brand of vodka
>> to "absolute". Thanks. (I've still not installed OboEdit.)
> (Maybe the CV and mapping file look much clearer with enough absolut)
> @Martin: I've changed terms 403 and 404, added value-types and added 
> percentage unit. Hopefully this merges with your local changes (if any).
> 
> Thanks,
> A.
> 
> 

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David Creasy
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