metadata-schema/json_schema/module/biomaterial/medical_history.json at 871577feb8ea5cda9f514776db3d6d468702236f · HumanCellAtlas/metadata-schema · GitHub

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{
    "$schema": "http://json-schema.org/draft-07/schema#",
    "description": "Information about the medical history of a donor.",
    "additionalProperties": false,
    "title": "Medical history",
    "name": "medical_history",
    "type": "object",
    "properties": {
        "describedBy":  {
            "description": "The URL reference to the schema.",
            "type": "string",
            "pattern" : "^(http|https)://schema.(.*?)humancellatlas.org/module/biomaterial/(([0-9]{1,}.[0-9]{1,}.[0-9]{1,})|([a-zA-Z]*?))/medical_history"
        },
        "schema_version": {
            "description": "The version number of the schema in major.minor.patch format.",
            "type": "string",
            "pattern": "^[0-9]{1,}.[0-9]{1,}.[0-9]{1,}$",
            "example": "4.6.1"
        },
        "alcohol_status": {
            "description": "Whether the individual is actively consuming, was formerly consuming or never consumed alcohol beverages",
            "type": "string",
            "enum": [
                "active",
                "former",
                "never"
            ],
            "user_friendly": "Alcohol status",
            "example": "Should be one of: active, former, never.",
            "bionetworks": ["gut", "oral and craniofacial", "musculoskeletal", "liver"]
        },
        "alcohol_type": {
            "description": "Types of alcoholic beverages the donor consumed.",
            "type": "array",
            "items": {
                "type": "string"
            },
            "user_friendly": "Alcohol type",
            "example": "beer; liquor; wine",
            "bionetworks": ["gut", "oral and craniofacial", "musculoskeletal", "liver"]
        },
        "alcohol_units": {
            "description": "Alcohol consumption of donor in alcohol units per week (strength (ABV) x volume (ml) ÷ 1,000).",
            "type": "number",
            "user_friendly": "Alcohol units",
            "minimum": 0,
            "example": "2.5; 15.2; 23",
            "bionetworks": ["gut", "oral and craniofacial", "musculoskeletal", "liver", "heart"]
        },
        "alcohol_usage_duration": {
            "description": "Number of years in which the donor consumed alcohol.",
            "type": "integer",
            "user_friendly": "Alcohol usage duration",
            "minimum": 0,
            "example": 5,
            "bionetworks": ["gut", "oral and craniofacial", "musculoskeletal", "liver"]
        },
        "medication": {
            "description": "Medication(s) the individual was taking at time of biomaterial collection.",
            "type": "array",
            "items": {
                "$ref": "module/ontology/medication_ontology.json"
            },
            "user_friendly": "Medication"
        },
        "smoking_status": {
            "description": "Whether the individual is actively, was formerly or never consumed smoking tobacco products like cigarettes, cigars, pipe etc.",
            "type": "string",
            "enum": [
                "active",
                "former",
                "never"
            ],
            "user_friendly": "Smoking status",
            "example": "Should be one of: active, former, never."
        },
        "smoking_pack_years": {
            "description": "Estimated number of packs (20 cigarettes) smoked per day multiplied by the number of years the individual was smoking.",
            "type": "number",
            "user_friendly": "Smoking pack years",
            "minimum": 0,
            "example": 4.55
        },
        "years_since_smoking_cessation": {
            "description": "If smoking status is 'former', specify the number of years since smoking cessation.",
            "type": "integer",
            "user_friendly": "Years since smoking cessation",
            "minimum": 0,
            "example": 12
        },
        "nutritional_state": {
            "description": "Nutritional state of individual at time of biomaterial collection.",
            "type": "string",
            "enum": [
                "normal",
                "fasting",
                "feeding tube removed"
            ],
            "user_friendly": "Nutritional state",
            "example": "Should be one of: normal, fasting, or feeding tube removed."
        },
        "test_results": {
            "description": "Results from medical tests performed on the individual.",
            "type": "string",
            "user_friendly": "Test results",
            "example": "lipid panel shows normal level of LDL (124 mg/dL); HIV, HBV, HCV: Negative"
        },
        "treatment": {
            "description": "Treatments the individual has undergone prior to biomaterial collection.",
            "type": "string",
            "user_friendly": "Treatments",
            "example": "Patient treated with antibiotics for a urinary tract infection; Patient treated with chemotherapy (Epirubicin, cisplatin, capecitabine) to treat stomach cancer"
        }
    },
    "allOf":
        [
            {
                "if": {
                    "properties": {
                        "smoking_status": {
                            "const": "active"
                        }
                    }
                },
                "then": {
                    "properties": {
                        "years_since_smoking_cessation": {
                            "maximum": 0
                        }
                    }
                }
            },
            {
                "if": {
                    "properties": {
                        "smoking_status": {
                            "const": "never"
                        }
                    }
                },
                "then": {
                    "properties": {
                        "years_since_smoking_cessation": {
                            "type": "null"
                        },
                        "smoking_pack_years": {
                            "maximum": 0
                        }
                    }
                }
            }
        ]
}