Specification document update

[bittremieux]

Updates in the specification document to proceed to mzQC v1.1:

mzQC schema

• Upgrade the JSON Schema version (Upgrade JSON Schema #261).
• Include softwareSettings (or similar) under analysisSoftware to record full provenance of how a software tool was used.
• Update the matrix metric type to include row and column names, and add according examples.

CV

• Mention that common UO terms are mirrored in the PSI-MS CV (UO term duplication in PSI-MS-CV effects minor (or major?) issue with semantic validation #245).
• Formalized metrics classification (Documentation on new metrics classification #323).

Using mzQC

• Revisit and document semantic validation checks.
• Provide guidelines on how to merge mzQC files (Provide guidelines on mzQC merging #235).

[bittremieux]

Matrix metric example:

{
    "name": "my matrix metric",
    "accession": "MS:4XXXX",
    "value": {
        "row_names": ["file1,", "file2", ...],
        "column_names": ["metric_1", "metric_2", ...]
        "data": [
            [1, 2, 3],
            [4, 5, 6]
        ]
    },
    "unit": {
        "name": "",
        "accession": "",
        "value": ""
    }
}

Additionally, change the current table metric example in the specification document to have mixed value types to clearly show the difference with a matrix metric.