Re: [Psidev-pi-dev] [HUPO-PSI/mzIdentML] Proteogenomics encoding (#4)

[F. G. <not...@gi...>]

I'm getting these errors when trying to validate the file using: mzIdentMLValidator_GUI_v1.4.16-SNAPSHOT

`
Message 1:
    Rule ID: PeptideLevelStatsObjectRule
    Level: ERROR
    Context(/MzIdentML/DataCollection/AnalysisData/SpectrumIdentificationList/SpectrumIdentificationResult/SpectrumIdentificationItem )
    --> The SpectrumIdentificationItem (id='SIR_3007_SII_2') element at /MzIdentML/DataCollection/AnalysisData/SpectrumIdentificationList/SpectrumIdentificationResult/SpectrumIdentificationItem doesn't contain the  triplet of terms MS:1002520 (peptide group ID), MS:1002500 (peptide passes threshold) and a child of MS:1002358 (search engine specific score for distinct peptides) required in case of peptide-level scoring
    Tip: Add the triplet of terms MS:1002520 (peptide group ID), MS:1002500 (peptide passes threshold) and a child of MS:1002358 (search engine specific score for distinct peptides) to each SpectrumIdentificationItem


Message 2:
    Rule ID: SpectrumIdentificationList_must_rule
    Level: ERROR
    Context(/cvParam/@accession ) in 2 locations
    --> None of the given CvTerms were found at '/MzIdentML/DataCollection/AnalysisData/SpectrumIdentificationList/cvParam/@accession' because no values were found:
  - Any children term of MS:1002438 (spectrum identification list result details). A single instance of this term can be specified. The matching value has to be the identifier of the term, not its name.


Message 3:
    Rule ID: ProteinDetectionList_must_rule
    Level: ERROR
    Context(/cvParam/@accession ) in 2 locations
    --> None of the given CvTerms were found at '/MzIdentML/DataCollection/AnalysisData/ProteinDetectionList/cvParam/@accession' because no values were found:
  - The sole term MS:1002404 (count of identified proteins) or any of its children. A single instance of this term can be specified. The matching value has to be the identifier of the term, not its name.
`

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