CIMAC-CIDC/cidc-schemas

{
  "$schema": "metaschema/strict_meta_schema.json#",
  "$id": "rna_assay-v0",
  "title": "RNA Gene Expression Assay version 0",
  "type": "object",
  "description": "Additional properties to describe a RNA assay for expression analysis.",
  "additionalProperties": false,
  "mergeStrategy": "objectMerge",
  
  "required": [
    "assay_creator",
    "enrichment_method",
    "records",
    "sequencer_platform"
  ],

  "allOf": [
    { "$ref": "assays/components/assay_core.json" },
    { "$ref": "assays/components/ngs_assay_core.json" }
  ],

  "properties": {
    "assay_creator": { "$ref": "assays/components/assay_core.json#properties/assay_creator" },
    "sequencer_platform": { "$ref": "assays/components/ngs_assay_core.json#properties/sequencer_platform" },
    "library_kit": { "$ref": "assays/components/ngs_assay_core.json#properties/library_kit" },
    "paired_end_reads": { "$ref": "assays/components/ngs_assay_core.json#properties/paired_end_reads" },

    "enrichment_method": {
      "description": "Method used for enriching for mRNA.",
      "type": "string",
      "enum": [
        "PolyA capture",
        "Transcriptome capture v1",
        "Transcriptome capture v6",
        "Ribo minus"
      ]
    },
    "enrichment_vendor_kit": {
      "description": "Vendor for the bait set used for enrichment, e.g. Twist, Agilent, IDT.",
      "type": "string",
      "enum": ["Agilent", "Twist", "IDT", "NEB", "Illumina - TruSeq Stranded PolyA mRNA", "Illumina - TruSeq Stranded mRNA Sample Prep Kit", "Illumina- TruSeq RNA Access Library Prep Kit"]
    },

    "records": {
      "type": "array",
      "description": "A single data record from RNAseq assay.",
      "mergeStrategy": "arrayMergeById",
      "mergeOptions": { "idRef": "cimac_id" },
      
      "items": {
        "additionalProperties": false,
        "type": "object",
        "mergeStrategy": "objectMerge",
        "allOf": [ { "$ref": "assays/components/ngs_assay_record.json" } ],
        
        "properties": {
          "cimac_id": { "$ref": "assays/components/ngs_assay_record.json#properties/cimac_id" },
          "files": { "$ref": "assays/components/ngs_assay_record.json#properties/files" },

          "library_yield_ng": {
            "description": "Resulting yield (in ng) from library construction.",
            "type": "number"
          },
          "dv200": {
            "description": "The percentage of fragments > 200 nucleotides. (0-1)",
            "type": "number",
            "minimum": 0,
            "maximum": 1
          },
          "rqs": {
            "description": "RNA quality score. (0-10)",
            "type": "number",
            "minimum": 0,
            "maximum": 10
          },
          "rin": {
            "description": "RNA integrity number. (0-10)",
            "type": "number",
            "minimum": 0,
            "maximum": 10
          },
          "quality_flag": {
            "description": "Flag used for quality.",
            "type": "number"
          }
        }
      }
    }
  }
}