[Psidev-pi-dev] validation of MPC_example.axml

[Martin E. <mar...@ru...>]

Hi Andreas, hi all,

Validating the MPC_example.axml I get the following validation errors (plus suggestion/comment):

Error: CV term used in invalid element: 'BTO:0000255 - brain cell line' at element
'/AnalysisXML/AnalysisSampleCollection/GenericMaterial'
For me, it seems, that the R5 rule cvIdentifierRef is wrong?: BTO instead of PSI-PI?

Error: CV term used in invalid element: 'PI:00194 - quality estimation with decoy database' at element
'/AnalysisXML/AnalysisProtocolCollection/ProteinDetectionProtocol/AnalysisParams'
In my point of view, PI:00194 and its children should be added to R24 with OR.

Error: Value of CVTerm not allowed: 'UO:0000169 - parts per million, value=75.0' at element
'/AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/ParentTolerance'
Error: Value of CVTerm not allowed: 'UO:0000221 - dalton, value=0.9' at element
'/AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/FragmentTolerance'
Error: Value of CVTerm not allowed: 'UO:0000221 - dalton, value=15.994914622' at element 
'/AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/ModificationParams/SearchModification'
Are these problems with . vs , (english vs. german decimal point?).
Where is the type declared?

Error: Value-type required, but not given (xsd:string): 'PI:00267 - software vendor, value=' at element
'/AnalysisXML/AnalysisSoftwareList/AnalysisSoftware/ContactRole/role'
I think, for software vendor is no value required. In the XML there is an Organization element 
containing the name and the CV term describes only the role without value.

Warning: No mapping rule found for element '/AnalysisXML/DataCollection/Inputs/SearchDatabase'
There should be a rule mapping this XPath to PI:00011 (search database details) (allow children).

Warning: Unknown CV term: 'NEWT:9606 - Homo sapiens' at element '/AnalysisXML/AnalysisSampleCollection/GenericMaterial'
Warning: Unknown CV term: 'PI-UNIMOD:3508 - Oxidation' at element '/AnalysisXML/SequenceCollection/Peptide/Modification'
I think these will be obsolete as soon as you link the obo files...

I haven't added these remarks to the issue list, please add those for which you don't agree to 
my respective suggestion ;-)

  Bye
    Martin