schema.json

{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$schema_version": "1.0",
    "additionalProperties": false,
    "properties": {
        "data": {
            "additionalProperties": false,
            "properties": {
                "id": {
                    "title": "FungToxins ID",
                    "type": "string",
                    "pattern": "^FT\\d{5}$"
                },
                "compound": {
                    "additionalProperties": false,
                    "properties": {
                        "main_name": {
                            "title": "Main compound name",
                            "type": "string"
                        },
                        "alt_names": {
                            "title": "Alternative compound names",
                            "type": "array",
                            "items": {
                                "type": "string"
                            }
                        },
                        "family": {
                            "title": "Compound family",
                            "type": "string"
                        },
                        "smiles": {
                            "title": "SMILES representation of compound structure",
                            "type": "string"
                        },
                        "mol_formula": {
                            "title": "Molecular formula",
                            "type": "string"
                        },
                        "mw_avg": {
                            "title": "Average molecular weight (also called full molecular weight)",
                            "type": "number",
                            "minimum": 0
                        },
                        "mw_mono": {
                            "title": "Monoisotopic molecular weight (also called exact molecular weight)",
                            "type": "number",
                            "minimum": 0
                        },
                        "databases": {
                            "additionalProperties": false,
                            "properties": {
                                "chembl": {
                                    "title": "ChEMBL identifier",
                                    "type": "string",
                                    "pattern": "^(CHEMBL\\d+|missing)$"
                                },
                                "npatlas": {
                                    "title": "NPAtlas identifier",
                                    "type": "string",
                                    "pattern": "^(NPA\\d{6}|missing)$"
                                },
                                "chemspider": {
                                    "title": "ChemSpider identifier",
                                    "type": "string",
                                    "pattern": "^(\\d+|missing)$"
                                },
                                "pubchem": {
                                    "title": "PubChem identifier",
                                    "type": "string",
                                    "pattern": "^(\\d+|missing)$"
                                }
                            }
                        }
                    },
                    "required":
                    [
                        "main_name",
                        "smiles",
                        "mol_formula",
                        "mw_avg",
                        "mw_mono",
                        "databases"
                    ]
                },
                "biosynthesis":{
                    "additionalProperties": false,
                    "properties": {
                        "gene_clusters": {
                            "title": "Known biosynthetic gene clusters that produce the compound",
                            "type": "array",
                            "items": {
                                "additionalProperties": false,
                                "properties": {
                                    "mibig_id": {
                                        "title": "MIBiG accession",
                                        "type": "string",
                                        "pattern": "^BGC\\d{7}$"
                                    },
                                    "mibig_class": {
                                        "title": "Biosynthetic class as represented in MIBiG",
                                        "type": "array",
                                        "items": {
                                            "type": "string"
                                        }
                                    },
                                    "organism": {
                                        "title": "The organism in which the BGC was found",
                                        "$ref": "#/$defs/organism"
                                    },
                                    "compounds": {
                                        "title": "All compounds reported to be produced by the BGC",
                                        "type": "array",
                                        "items": {
                                            "type": "string"
                                        }
                                    },
                                    "status": {
                                        "title": "Status of the entry (pending, active or retired)",
                                        "enum": [
                                            "pending",
                                            "active",
                                            "retired"
                                        ]
                                    },
                                    "completeness": {
                                        "title": "Whether the BGC is reported as complete",
                                        "enum": [
                                            "incomplete",
                                            "complete",
                                            "unknown"
                                        ]
                                    },
                                    "minimal": {
                                        "title": "Whether this is a minimal entry",
                                        "type": "boolean"
                                    }
                                },
                                "required": [
                                    "mibig_id",
                                    "mibig_class",
                                    "organism",
                                    "compounds",
                                    "status",
                                    "completeness",
                                    "minimal"
                                ]
                            }
                        },
                        "producers": {
                            "title": "Organisms reported to produce the compound",
                            "type": "array",
                            "items": {
                                "additionalProperties": false,
                                "properties": {
                                    "organism": {
                                        "title": "Organism reported to produce the compound",
                                        "$ref": "#/$defs/organism"
                                    },
                                    "ref_id": {
                                        "title": "Reference ID for the associated publication",
                                        "$ref": "#/$defs/ref_id"
                                    }
                                },
                                "required": [
                                    "organism",
                                    "ref_id"
                                ]
                            }
                        }
                    },
                    "required": [
                        "gene_clusters",
                        "producers"
                    ]
                },
                "toxicity":{
                    "additionalProperties": false,
                    "properties": {
                        "experimental_data": {
                            "title": "Experimental data showing toxic effects of the compound",
                            "type": "array",
                            "items": {
                                "additionalProperties": false,
                                "properties": {
                                    "toxicity_type": {
                                        "title": "The type of toxicity found",
                                        "$ref": "#/$defs/toxicity_type"
                                    },
                                    "ref_id": {
                                        "title": "Reference ID for the associated publication",
                                        "$ref": "#/$defs/ref_id"
                                    }
                                },
                                "required": [
                                    "toxicity_type",
                                    "ref_id"
                                ]
                            }
                        },
                        "carcinogenicity": {
                            "title": "Carcinogenicity as evaluated by the International Agency for Research on Cancer (IARC)",
                            "additionalProperties": false,
                            "properties": {
                                "IARC_group": {
                                    "title": "IARC classification",
                                    "enum": [
                                        "1",
                                        "2A",
                                        "2B",
                                        "3",
                                        "missing"
                                    ]
                                },
                                "agent": {
                                    "title": "Name of the compound or compound group evaluated by the IARC",
                                    "type": "string"
                                },
                                "volume": {
                                    "title": "Volume of IARC Monographs",
                                    "type": "string"
                                },
                                "vol_year": {
                                    "title": "Year that this volume was published",
                                    "type": "string"
                                },
                                "eval_year": {
                                    "title": "Year that the agent was evaluated",
                                    "type": "string"
                                }
                            },
                            "required": [
                                "IARC_group",
                                "agent",
                                "volume",
                                "vol_year",
                                "eval_year"
                            ]
                        },
                        "databases": {
                            "additionalProperties": false,
                            "properties": {
                                "comptox": {
                                    "title": "CompTox identifier (DTXCID - Compound ID or DTXSID - Substance ID)",
                                    "type": "string",
                                    "pattern": "^(DTX(C|S)ID\\d+|missing)$"
                                },
                                "ctd": {
                                    "title": "Comparative Toxicogenomics Database identifier (MeSH ID)",
                                    "type": "string",
                                    "pattern": "^((C|D)\\d{6}|missing)$"
                                }
                            }
                        }
                    },
                    "required": [
                        "experimental_data",
                        "carcinogenicity",
                        "databases"
                    ]
                },
                "notes":{
                    "title": "Extra comments for this compound",
                    "type": "array",
                    "items": {
                        "type": "string"
                    }
                }
            },
            "required": [
                "id",
                "compound",
                "biosynthesis",
                "toxicity"
            ]
        }
    },
    "$defs": {
        "organism": {
            "additionalProperties": false,
            "properties": {
                "organism_name": {
                    "title": "Name of the organism",
                    "type": "string"
                },
                "taxid": {
                    "title": "NCBI taxid of the organism",
                    "type": "string",
                    "pattern": "^(\\d+|missing)$"
                },
                "category": {
                    "title": "Whether the organism is a bacterium, fungus or plant",
                    "enum": [
                        "bacteria",
                        "fungi",
                        "plants",
                        "other"
                    ]
                }
            },
            "required": [
                "organism_name",
                "taxid",
                "category"
            ]
        },
        "ref_id": {
            "type": "array",
            "items": {
                "type": "string",
                "pattern": "^REF\\d{5}$"
            }
        },
        "toxicity_type": {
            "enum": [
                "anorexigenic",
                "appetite inducing",
                "carcinogenic",
                "cardiotoxic",
                "cytotoxic",
                "dermatoxic",
                "embryotoxic",
                "emetic",
                "genotoxic",
                "growth inhibiting",
                "hematotoxic",
                "hepatotoxic",
                "immunosuppressive",
                "lienotoxic",
                "mutagenic",
                "nephrotoxic",
                "neurotoxic",
                "pro-inflammatory",
                "psychoactive (depressant)",
                "psychoactive (hallucinogen)",
                "psychoactive (other)",
                "psychoactive (stimulant)",
                "teratogenic",
                "toxic to muscles",
                "toxic to the cardiovascular system",
                "toxic to the gastrointestinal system",
                "toxic to the reproductive system",
                "toxic to the respiratory system",
                "tremorgenic",
                "vasoconstrictive",
                "xenoestrogenic"
            ]
        }
    }
}