upload-metadata.schema.json

{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "http://qbic.life/v1/upload-metadata.schema.json",
    "title": "Upload metadata for data registration at QBiC",
    "description": "A full description of mandatory and optional metadata properties that need to/can be included for data registration via QBiC dropboxes.",
    "type": "object",
    "definitions": {
        "qc": {
            "type": "object",
            "properties": {
                "qcml_id": {
                    "type": "string",
                    "description": "A qcml id following the qzml specification",
                    "pattern": "^QC:[0-9]{7}$"
                }, 
                "name": {
                    "type": "string",
                    "description": "Name of the quality control",
                    "examples": ["read count", "target region read depth", "Q20 read percentage"]
                },
                "value": {
                    "type": "string",
                    "description": "The actual qc value"
                }
            }
        },
        "sample": {
            "type": "object",
            "properties": {
                "genome": {
                    "type": "string",
                    "examples": ["GRCh37"]
                },
                "id_genetics": {
                    "type": "string",
                    "description": "A sample URI provided by the human genetics department",
                    "examples": ["GS000000_01"]
                },
                "id_qbic": {
                    "type": "string",
                    "pattern": "Q\\w{4}\\d{3}[A-X][A-X0-9]",
                    "description": "QBIC sample code of the analysed biological specimen",
                    "examples": ["QTEST001AE"]
                },
                "processing_system": {
                    "type": "string",
                    "examples": ["SureSelectXT Human All Exon v5"]
                },
                "qc": {
                    "type": "array",
                    "items": {
                        "allOf": [
                            {
                                "$ref": "#/definitions/qc"
                            }
                        ]
                    }
                }, 
                "tumor": {
                    "type": "string",
                    "enum": ["yes", "no"]
                }
            }
        }
    },
    "properties": {
        "files": {
            "type": "array",
            "items": { "type": "string" },
            "minItems": 1
        },
        "type": {
            "type": "string",
            "enum": ["dna_seq", "rna_seq", "dna_seq_somatic"]
        },
        "sample1": { "$ref": "#/definitions/sample" }, 
        "sample2": { "$ref": "#/definitions/sample" }
    },
    "required": [
        "files", 
        "type",
        "sample1"
    ] 
}