psidev-pi-dev

[Psidev-pi-dev] [HUPO-PSI/mzIdentML] Validation issues with mzidLib_Rosetta2a_Ecoli_spectra_msgfplus_fdr_threshold_groups.mzid (#39)

[Eric D. <not...@gi...>]

SchemaLocation is http://www.psidev.info/files/mzIdentML1.1.0.xsd
ERROR: cvParam PSM-level q-value should have units, but it does not!
WARNING: MS:1001062 should be 'Mascot MGF format' instead of 'Mascot MGF file'
WARNING: MS:1001189 should be 'modification specificity peptide N-term' instead of 'modification specificity N-term'
WARNING: MS:1002241 should be 'mzidLib:ProteoGrouper' instead of 'ProteoGrouper'
WARNING: MS:1002404 should be 'count of identified proteins' instead of 'count of identified protein'


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Re: [Psidev-pi-dev] [HUPO-PSI/mzIdentML] Validation issues with mzidLib_Rosetta2a_Ecoli_spectra_msgfplus_fdr_threshold_groups.mzid (#39)

[andrewrobertjones <not...@gi...>]

@germa Please can we update the q-value term (below). Both of the units are wrong, I'm pretty sure there are no suitable units for a q-value.

Thanks Andy

[Term]
id: MS:1002354
name: PSM-level q-value
def: "Estimation of the q-value for peptide spectrum matches." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002347 ! PSM-level identification confidence metric
relationship: has_units UO:0000166 ! parts per notation unit
relationship: has_units UO:0000187 ! percent
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

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Re: [Psidev-pi-dev] [HUPO-PSI/mzIdentML] Validation issues with mzidLib_Rosetta2a_Ecoli_spectra_msgfplus_fdr_threshold_groups.mzid (#39)

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

I have update the example file. @edeutsch can you please re-run the validator. Thanks. Fawaz

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Re: [Psidev-pi-dev] [HUPO-PSI/mzIdentML] Validation issues with mzidLib_Rosetta2a_Ecoli_spectra_msgfplus_fdr_threshold_groups.mzid (#39)

[Gerhard M. <not...@gi...>]

Removed the units from the FDR and q-value terms in version 3.90.0 of psi-ms.obo

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