{ "$id":                          "https://schemas.mpai.community/TFA/V1.5/data/GenomicsOmicsQualifier.json",
  "$schema":                      "https://json-schema.org/draft/2020-12/schema",

  "title":                        "Genomics Omics Qualifier V1.5",
                                  "description": "Genomics/Omics Sub-Type groups, Format groups, and allowed pairings.",
                                  "type": "object",
                                  "required": [ "subTypes", "formats", "groupMap", "DataExchangeMetadata", "Trace" ],
                                  "additionalProperties": false, "properties": {

    "subTypes":                   { "type": "object", "additionalProperties": false,
                                    "required": [ "DNA-Based Data", "RNA-Based Data", "Epigenomic Data", "Proteomics Data", "Metabolomics Data" ],
                                    "properties": {

      "DNA-Based Data":           { "type": "array", "items": { "type": "string" }, "minItems": 1, "uniqueItems": true,
                                    "default": [ "Whole-genome variants", "Whole-exome variants", "Targeted panel variants",
                                      "Structural variants", "Copy-number profiles" ] },

      "RNA-Based Data":           { "type": "array", "items": { "type": "string" }, "minItems": 1, "uniqueItems": true,
                                    "default": [ "Gene-expression matrix (bulk RNA-seq)", "Transcript-level quantification",
                                      "Splicing / junction counts" ] },

      "Epigenomic Data":          { "type": "array", "items": { "type": "string" }, "minItems": 1, "uniqueItems": true,
                                    "default": [ "Methylation array profiles", "Bisulfite sequencing profiles" ] },

      "Proteomics Data":          { "type": "array", "items": { "type": "string" }, "minItems": 1, "uniqueItems": true,
                                    "default": [ "Protein abundance profiles", "Peptide quantification tables" ] },

      "Metabolomics Data":        { "type": "array", "items": { "type": "string" }, "minItems": 1, "uniqueItems": true,
                                    "default": [ "Metabolite abundance profiles" ] } } },

    "formats":                    { "type": "object", "additionalProperties": false,
                                    "required": [ "DNA-Based Formats", "RNA-Based Formats", "Epigenomic Formats", "Proteomics Formats", "Metabolomics Formats" ],
                                    "properties": {

      "DNA-Based Formats":        { "type": "array", "items": { "type": "string" }, "minItems": 1, "uniqueItems": true,
                                    "default": [ "VCF", "BCF", "FASTQ (raw reads)", "BAM / CRAM (aligned reads)",
                                      "TSV/CSV (variant tables)" ] },

      "RNA-Based Formats":        { "type": "array", "items": { "type": "string" }, "minItems": 1, "uniqueItems": true,
                                    "default": [ "FASTQ (raw reads)", "BAM / CRAM", "TSV/CSV (gene-expression matrices)",
                                      "HDF5 (assay containers)" ] },

      "Epigenomic Formats":       { "type": "array", "items": { "type": "string" }, "minItems": 1, "uniqueItems": true,
                                    "default": [ "IDAT (array raw files)", "TSV/CSV (processed methylation profiles)",
                                      "HDF5" ] },

      "Proteomics Formats":       { "type": "array", "items": { "type": "string" }, "minItems": 1, "uniqueItems": true,
                                    "default": [ "TSV/CSV (protein/peptide quantification)", "HDF5" ] },

      "Metabolomics Formats":     { "type": "array", "items": { "type": "string" }, "minItems": 1, "uniqueItems": true,
                                    "default": [ "TSV/CSV (metabolite abundance)", "HDF5" ] } } },

    "groupMap":                   { "type": "array", "minItems": 1, "items": { "type": "object", "additionalProperties": false,
                                    "required": [ "subTypeGroup", "formatGroup" ], "properties": {
      "subTypeGroup":             { "type": "string" },
      "formatGroup":              { "type": "string" } } },
                                    "default": [
                                      { "subTypeGroup": "DNA-Based Data",        "formatGroup": "DNA-Based Formats" },
                                      { "subTypeGroup": "RNA-Based Data",        "formatGroup": "RNA-Based Formats" },
                                      { "subTypeGroup": "Epigenomic Data",       "formatGroup": "Epigenomic Formats" },
                                      { "subTypeGroup": "Proteomics Data",       "formatGroup": "Proteomics Formats" },
                                      { "subTypeGroup": "Metabolomics Data",     "formatGroup": "Metabolomics Formats" } ] },

    "DataExchangeMetadata":       { "$ref": "https://schemas.mpai.community/AIF/V3.0/data/DataExchangeMetadata.json" },
    "Trace":                      { "$ref": "https://schemas.mpai.community/AIF/V3.0/data/Trace.json" },
    "DescrMetadata":              { "type": "string", "maxLength": 2048 } } }