[Psidev-pi-dev] [HUPO-PSI/mzIdentML] combined_fdr_1.2.mzid validation issues (#35)

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

My CV term validator finds these issues with this file:
ERROR: cvParam distinct peptide-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:1001400 should be 'OMSSA xml format' instead of 'OMSSA xml file'
WARNING: MS:1002439 should be 'final PSM list' instead of 'final PSM list UNDER DISCUSSION'

the first error may be an error in the CV. I don't think we want units for q-value in the term? Should we remove units from all q-value terms? This issue affects several.

[Term]
id: MS:1001868
name: distinct peptide-level q-value
def: "Estimation of the q-value for distinct peptides once redundant identifications of the same peptide have been removed (id e
st multiple PSMs, possibly with different mass modifications, mapping to the same sequence have been collapsed to one entry)." [
PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002484 ! peptide-level statistical threshold
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


---
You are receiving this because you are subscribed to this thread.
Reply to this email directly or view it on GitHub:
https://github.com/HUPO-PSI/mzIdentML/issues/35