UO term duplication in PSI-MS-CV effects minor (or major?) issue with semantic validation

[mwalzer]

If a .mzqc uses unit terms and lists UO as one of the ControlledVocabularies, e.g.

    "controlledVocabularies": [
      {
        "name": "Proteomics Standards Initiative Mass Spectrometry Ontology",
        "uri": "https://github.com/HUPO-PSI/psi-ms-CV/releases/download/v4.1.186/psi-ms.obo",
        "version": "4.1.186"
      },
      {
        "name": "Unit Ontology",
        "uri": "https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/v2023-05-23/unit-ontology.obo",
        "version": "v2023-05-23"
      }
    ]

The issue will be:

vscode@dab2d5d09534:/workspaces/pymzqc$ python mzqcaccessories/offlinevalidator/mzqc_offline_validator.py tests/examples/individual-runs.mzQC 
{
    "input files": [],
    "label uniqueness": [],
    "metric use": [],
    "ontology load errors": [],
    "ontology term errors": [
        "Ambiguous CVTerms of severity 6 and message: term found in multiple vocabularies = Term('UO:0000189', name='count unit'),Term('UO:0000189', name='count unit')",
        "Ambiguous CVTerms of severity 6 and message: term found in multiple vocabularies = Term('UO:0000189', name='count unit'),Term('UO:0000189', name='count unit')",
        "Ambiguous CVTerms of severity 6 and message: term found in multiple vocabularies = Term('UO:0000189', name='count unit'),Term('UO:0000189', name='count unit')",
        "Ambiguous CVTerms of severity 6 and message: term found in multiple vocabularies = Term('UO:0000010', name='second'),Term('UO:0000010', name='second')"
    ],
    "schema validation": "success"
}

[mwalzer]

If a file uses vocabularies with overlapping terms (name and id), I'd consider this a major issue, but in the unit instance of our schema, not so much...
still, I would not want to hardcode some exception for the duplications in the validator.

[mwalzer]

omission of the UO in ControlledVocabularies yields validation success, of course

[bittremieux]

We should document on the website that UO terms are replicated in the PSI-MS CV and that those should be preferred if available to avoid the issue with duplicate definitions.