[Psidev-qc-dev] QuaMeter ID-free mzQC example

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

I have updated the mzQC example with QuaMeter ID-free metrics here: https://gist.github.com/bittremieux/a3a43ce929e38fd0230005782f3c9725

Please check it out and provide any feedback.

I had a few open questions:

  *   @Dave: I'm still missing the unit for metric "XIC-FWHM quantiles"<https://github.com/HUPO-PSI/mzQC/blob/master/cv/qc-cv.obo#L212>. What would be the correct unit there?
  *   Some of the metric values are "log ratios". I have now used "ratio" as unit for these metrics because I couldn't find a log ratio term in the Unit Ontology. Is this correct?
  *   Please have a look at the table metrics "MS2 known precursor charges fractions" and "MS2 unknown and likely precursor charges fractions". The column headers are terms from the Unit Ontology ("Charge state" and "Fraction"), as also described in the specification document in section 4.1.1 on page 11 ("table column type definitions"). This defines the unit of the table's columns, as specified, but by not explicitly including the term's accession and only using the name, the link to a controlled vocabulary is lost in the mzQC file. Should we maybe repeat the units for tables as a "unit" element as well? For example, current:

{
    "accession": "QC:4000063",
    "name": "MS2 known precursor charges fractions",
    "value": {
        "Charge state": [
        "1",
        "2",
        "3",
        "4",
        "5",
        "6"
        ],
        "Fraction": [
        0,
        0.6830609999999999,
        0.305012,
        0.00844278,
        0.00134012,
        0.0021441999999999998
        ]
    }
}

Alternative:

{
    "accession": "QC:4000063",
    "name": "MS2 known precursor charges fractions",
    "value": {
        "Charge state": [
        "1",
        "2",
        "3",
        "4",
        "5",
        "6"
        ],
        "Fraction": [
        0,
        0.6830609999999999,
        0.305012,
        0.00844278,
        0.00134012,
        0.0021441999999999998
        ]
    },
    "unit": [
        {
            "accession": "MS:1000041",
            "name": "charge state"
        },
        {
            "accession": "UO:0000191",
            "name": "fraction"
        }
    ]
}


Maybe the latter was our intention already, because "unit" is allowed to be an array according to the JSON Schema and specification document. If so, we should clarify in the specification document how table units should be a list that matches the column order.

Thank you for having a look at these questions.

Best,
Wout