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

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

Yes, as far as I read the spec both versions are compliant, as units for table metrics don't really seem unambiguously described currently. Possibly an oversight because we didn't have a proper example of this yet? I think the second version is more in line with units for other metric types though and is more descriptive. We'll need to properly include this in the spec then.

One other comment is that I now used terms from the Unit Ontology as units. There are also terms in our QC-CV that are the same except that they're wrappers for those units to be used as table columns. See for example "fraction (UO:0000191)<https://github.com/bio-ontology-research-group/unit-ontology/blob/master/unit.obo#L2469>" vs "Fraction (QC:4000239)<https://github.com/HUPO-PSI/mzQC/blob/master/cv/qc-cv.obo#L1884>". I have forgotten the previous discussion about this. What is the advantage of introducing new CV terms for these units? @Julian maybe? To be able to do a semantic check that these explicitly are column headers? I don't really see a strong reason to have to duplicate CV terms when used as column labels.

Best,
Wout
________________________________
From: David TABB <dav...@pa...>
Sent: Wednesday, June 9, 2021 4:32
To: Bittremieux, Wout <wbi...@he...>
Subject: RE: QuaMeter ID-free mzQC example


Hi, Wout.  Very nice work!



The XIC-FWHM values are peak widths, measured in seconds.



Ratio rather than log ratio will be fine, since that’s what we have available.  Of course, a 1:1 ratio is 1.0 in linear space rather than 0.0 in log space, but c’est la vie.



I think of the precursor charge states as being a “proportion,” where the sum of all equals 1.0 rather than a “percentage,” where the sum is 100%, or a “fraction,” where the sum is arbitrary.  I think that level of nuance is unnecessary to resolve for this example, though.



I like the variation where you include the unit types for each column in the trailer, but do both of these formattings comply with the spec as written?



Thank you,

Dave



From: Bittremieux, Wout via Psidev-qc-dev <psi...@li...>
Sent: Wednesday, June 9, 2021 2:31 AM
To: psi...@li...
Subject: [Psidev-qc-dev] QuaMeter ID-free mzQC example



Dear colleagues,



I have updated the mzQC example with QuaMeter ID-free metrics here: https://gist.github.com/bittremieux/a3a43ce929e38fd0230005782f3c9725<https://urldefense.com/v3/__https:/gist.github.com/bittremieux/a3a43ce929e38fd0230005782f3c9725__;!!JFdNOqOXpB6UZW0!_5wyaFE5AqXlNGS7vHPlkoz7VZM5nQpv_sePdYjmUqyoFjOH98anwTWamNToUEQ$>



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://urldefense.com/v3/__https:/github.com/HUPO-PSI/mzQC/blob/master/cv/qc-cv.obo*L212__;Iw!!JFdNOqOXpB6UZW0!_5wyaFE5AqXlNGS7vHPlkoz7VZM5nQpv_sePdYjmUqyoFjOH98anwTWaQKpTz5s$>. 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