{
    "$schema": "http://json-schema.org/schema#",
    "description": "schema for a the json that describes the registration activity.",
    "version": "3.0",
    "type": "object",
    "required": [
        "registration",
        "activities",
        "observations",
        "agents"
    ],
    "properties": {
        "registration": {
            "type": "object",
            "description": "Registration activity, regrouping all activities described in file.",
            "properties": {
                "id": {
                    "$ref": "#/definitions/uuid"
                },
                "comment": {
                    "type":"string"
                },
                "submission_date": {
                    "description": "An RFC3339 date in the format YYYY-MM-DD.",
                    "type": "string",
                    "format": "date",
                    "pattern": "^(19|20)\\d\\d-(0[1-9]|1[012])-(0[1-9]|[12][0-9]|3[01])$"
                },
                "data_providers": {
                    "description": "List of organisations and/or contributors who contributed the data.",
                    "type": "array",
                    "minItems": 1,
                    "items": {
                        "type": "object",
                        "properties": {
							"id": {
								"type": "string"
							}
						}
                    }
                },
                "release": {
                    "enum": [
                        "HBP",
                        "public"
                    ]
                }
            }
        },
        "resources": {
            "description": "List of the data sources used in the registration. Those data sources are typically files or databases that represent the results of the observations.",
            "type": "array",
            "items": {
                "type": "object",
                "required": [
                    "id",
                    "mime_type",
                    "address"
                ],
                "properties": {
                    "id": {
                        "$ref": "#/definitions/uuid"
                    },
                    "address": {
                        "description": "A resolvable URI",
                        "type": "string"
                    },
                    "mime_type": {
                        "description": "Link to mime type service.",
                        "$ref": "#/definitions/xref"
                    },
                    "represented_entities": {
                        "type": "array",
                        "description": "Entities found in the representation of the data. E.g. cells found in image of the slice.",
                        "items": {
                            "$ref": "#/definitions/uuid"
                        }
                    },
                    "generation": {
                        "description": "UUID of the activity that generated the representation. Must be described in the same registration file.",
                        "$ref": "#/definitions/uuid"
                    }
                }
            }
        },
        "activities": {
            "description": "List of registered activities.",
            "type": "array",
            "minItems": 1,
            "items": {
                "description": "Representation of a HBP-Provenance activity.",
                "type": "object",
                "required": [
                    "id",
                    "type",
                    "end_date",
                    "agents",
                    "plan",
                    "source_entities"
                ],
                "properties": {
                    "id": {
                        "$ref": "#/definitions/uuid"
                    },
                    "name": {
                        "type": "string"
                    },
                    "comment": {
                        "type":"string"
                    },
                    "type": {
                        "$ref": "#/definitions/onto_term"
                    },
                    "start_date": {
                        "description": "An RFC3339 date in the format YYYY-MM-DD.",
                        "type": "string",
                        "format": "date",
                        "pattern": "^(19|20)\\d\\d-(0[1-9]|1[012])-(0[1-9]|[12][0-9]|3[01])$"
                    },
                    "end_date": {
                        "description": "An RFC3339 date in the format YYYY-MM-DD. If end_date is not know, put the submission date of registration.",
                        "type": "string",
                        "format": "date",
                        "pattern": "^(19|20)\\d\\d-(0[1-9]|1[012])-(0[1-9]|[12][0-9]|3[01])$"
                    },
                    "agents": {
                        "description": "List of agent ids that were associated with the activity.",
                        "type": "array",
                        "minItems": 1,
                        "items": {
                            "type": "object",
                            "properties": {
                                "id": {
                                    "type": "string"
                                },
                                "role": {
                                    "$ref": "#/definitions/onto_term"
                                }
                            }
                        }
                    },
                    "protocol": {
                        "$ref": "#/definitions/onto_term"
                    },
                    "source_entities": {
                        "description": "An array containing the identifiers for input entities. The entities might be described in the current file or already in repository.",
                        "type": "array",
                        "minItems": 1,
                        "items": {
                            "$ref": "#/definitions/uuid"
                        }
                    }
                }
            }
        },
        "agents": {
            "description": "list of all agents associated with the activities described in the registration.",
            "type": "object",
            "properties": {
                "contributors": {
                    "description": "An array of people who contributed to the activities.",
                    "type": "array",
                    "minItems": 1,
                    "items": {
                        "type": "object",
                        "required": [
                            "id"
                        ],
                        "properties": {
                            "id": {
                                "type": "string"
                            },
                            "name": {
                                "type": "string"
                            },
                            "email": {
                                "type": "string"
                            }
                        }
                    }
                },
                "organisations": {
                    "description": "An array of organisations who contributed to the activities.",
                    "type": "array",
                    "minItems": 1,
                    "items": {
                        "type": "object",
                        "required": [
                            "id"
                        ],
                        "properties": {
                            "id": {
                                "type": "string"
                            },
                            "name": {
                                "type": "string"
                            }
                        }
                    }
                },
                "software": {
                    "description": "An array of software products used to generate data artifacts.",
                    "type": "array",
                    "minItems": 1,
                    "items": {
                        "type": "object",
                        "required": [
                            "id"
                        ],
                        "properties": {
                            "id": {
                                "type": "string"
                            },
                            "name": {
                                "type": "string"
                            },
                            "version": {
                                "type": "string"
                            }
                        }
                    }
                }
            }
        },
        "specimen": {
            "description": "An individual animal, plant, or single-celled life form.",
            "type": "array",
            "minItems": 1,
            "items": {
                "type": "object",
                "required": [
                    "id",
                    "name",
                    "sex",
                    "species",
                    "age"
                ],
                "properties": {
                    "id": {
                        "$ref": "#/definitions/uuid"
                    },
                    "name": {
                        "type": "string"
                    },
                    "comment": {
                        "type": "string"
                    },
                    "age": {
                        "description": "",
                        "type": "object",
                        "required": [
                            "period",
                            "value"
                        ],
                        "properties": {
                            "period": {
                                "enum": [
                                    "Gestation",
                                    "Post-natal"
                                ]
                            },
                            "value": {
                                "description": "Age in days.",
                                "type": "number",
                                "format": "float"
                            }
                        },
                        "comment": {
                            "type": "string"
                        }
                    },
                    "developmental_stage": {
                        "$ref": "#/definitions/onto_term"
                    },
                    "sex": {
                        "$ref": "#/definitions/onto_term"
                    },
                    "species": {
                        "$ref": "#/definitions/onto_term"
                    },
                    "strain": {
                        "$ref": "#/definitions/onto_term"
                    },
                    "transgenic": {
                        "$ref": "#/definitions/onto_term"
                    },
                    "disease": {
                        "$ref": "#/definitions/onto_term"
                    }
                }
            }
        },
        "samples": {
            "description": "Biological material.",
            "type": "array",
            "minItems": 1,
            "items": {
                "type": "object",
                "required": [
                    "generation",
                    "id",
                    "name"
                ],
                "properties": {
                    "id": {
                        "$ref": "#/definitions/uuid"
                    },
                    "name": {
                        "type": "string"
                    },
                    "comment": {
                        "type": "string"
                    },
                    "generation": {
                        "description": "UUID of the activity that generated the sample. Must be described in the same registration file.",
                        "$ref": "#/definitions/uuid"
                    },
                    "brain_regions": {
                        "description": "Brain region(s) where the sample originates.",
                        "type": "array",
                        "items": {
                            "$ref": "#/definitions/onto_term"
                        }
                    }
                }
            }
        },
        "datasets": {
            "description": "List of generated observations to be registered.",
            "type": "array",
            "minItems": 1,
            "items": {
                "type": "object",
                "required": [
                    "id",
                    "categories",
                    "name",
                    "generation",
                    "representations"
                ],
                "properties": {
                    "id": {
                        "$ref": "#/definitions/uuid"
                    },
                    "name": {
                        "type": "string"
                    },
                    "comment": {
                        "type": "string"
                    },
                    "categories": {
                        "type": "array",
                        "description": "The description of the nature of the data in neuroscientific terms.",
                        "minItems": 1,
                        "items": {
                            "$ref": "#/definitions/onto_term"
                        }
                    },
                    "generation": {
                        "description": "UUID of the activity that generated the observation. Must be described in the same registration file.",
                        "$ref": "#/definitions/uuid"
                    },
                    "brain_regions": {
                        "description": "Brain region(s) this observation was made on.",
                        "type": "array",
                        "items": {
                            "$ref": "#/definitions/onto_term"
                        }
                    },
                    "atlas_location": {
                        "description": "Details for registering the observation in a reference atlas.",
                        "type": "object",
                        "required": [
                            "bounding_box"
                        ],
                        "oneOf": [
                            {
                                "properties": {
                                    "atlas_template": {
                                        "description": "Reference atlas to which the observation was aligned. Can be itself.",
                                        "$ref": "#/definitions/uuid"
                                    },
                                    "is_template": {
                                        "type": "string"
                                    },
                                    "parent_space": {
                                        "description": "Parent space from which a bounding box was extracted. Reference the Knowledge Graph UUID of the parent observation.",
                                        "$ref": "#/definitions/uuid"
                                    }
                                }
                            }
                        ],
                        "properties": {
                            "bounding_box": {
                                "description": "Coordinates of a bounding box in a reference space where the observation was extracted.",
                                "$ref": "#/definitions/bounding_box"
                            },
                            "transformation": {
                                "description": "Transformation to place the current bounding box in the atlas template specified.",
                                "type": "object",
                                "properties": {
                                    "transformation_type": {
                                        "enum": [
                                            "linear",
                                            "polynom"
                                        ]
                                    },
                                    "transformation_matrix": {
                                        "description":"3D matrix, ordered row."
                                        "type": "array",
                                        "items": {
                                            "type": "number",
                                            "format": "float"
                                        }
                                    }
                                }
                            }
                        }
                    },
                    "representations": {
                        "type": "array",
                        "minItems": 1,
                        "items": {
                            "$ref": "#/definitions/uuid"
                        }
                    }
                }
            }
        },
        "models": {
            "description": "In silico models, used to perform simulations and in silico experimentation.",
            "type": "array",
            "minItems": 1,
            "items": {
                "type": "object",
                "required": [
                    "id",
                    "categories",
                    "name",
                    "generation",
                    "representations"
                ],
                "properties": {
                    "id": {
                        "$ref": "#/definitions/uuid"
                    },
                    "name": {
                        "type": "string"
                    },
                    "comment": {
                        "type": "string"
                    },
                    "categories": {
                        "type": "array",
                        "description": "The description of the nature of the model in neuroscientific terms.",
                        "minItems": 1,
                        "items": {
                            "$ref": "#/definitions/onto_term"
                        }
                    },
                    "generation": {
                        "description": "UUID of the activity that generated the model. Must be described in the same registration file.",
                        "$ref": "#/definitions/uuid"
                    },
                    "locations": {
                        "description": "Brain region(s) from which the model was derived.",
                        "type": "array",
                        "items": {
                            "$ref": "#/definitions/onto_term"
                        }
                    },
                    "representations": {
                        "type": "array",
                        "minItems": 1,
                        "items": {
                            "$ref": "#/definitions/uuid"
                        }
                    }
                }
            }
        },
        "classifications": {
            "description": "A list of classification terms derived from a manual or automated analysis.",
            "type": "array",
            "minItems": 1,
            "items": {
                "type": "object",
                "required": [
                    "classification",
                    "generation"
                ],
                "properties": {
                    "classification": {
                        "$ref": "#/definitions/onto_term"
                    },
                    "generation": {
                        "description": "UUID of the activity that generated the classification. Must be described in the same registration file.",
                        "$ref": "#/definitions/uuid"
                    }
                }
            }
        }
    },
    "definitions": {
        "onto_term": {
            "description": "Reference to a resolvable ontology term.",
            "type": "object",
            "required": [
                "uri"
            ],
            "properties": {
                "uri": {
                    "description": "Resolvable URI for the ontology term, eg ontology.humanbrainproject.eu/$ontology_name/$term_code.",
                    "type": "string"
                },
                "name": {
                    "description": "Human readable name for the term.",
                    "type": "string"
                },
                "description": {
                    "description": "Human readable description for the term.",
                    "type": "string"
                }
            }
        },
        "uuid": {
            "type": "string",
            "pattern": "^[0-9a-fA-F]{8}-([0-9a-fA-F]{4}-){3}[0-9a-fA-F]{12}$"
        },
        "bounding_box": {
            "description": "XYZ coordinates of an axis-aligned bounding box in a reference space. The box is defined by at least 2 points.",
            "type": "object",
            "required": [
                "points"
            ],
            "properties": {
                "points": {
                    "description": "The lower and upper coordinate of the bounding box.",
                    "type": "array",
                    "minItems": 2,
                    "maxItems": 2,
                    "items": {
                        "type": "object",
                        "required": [
                            "x",
                            "y",
                            "z"
                        ],
                        "properties": {
                            "x": {
                                "type": "number",
                                "format": "float"
                            },
                            "y": {
                                "type": "number",
                                "format": "float"
                            },
                            "z": {
                                "type": "number",
                                "format": "float"
                            }
                        }
                    }
                },
                "resolution": {
                    "description": "Resolution in each dimension",
                    "type": "object",
                    "required": [
                        "unit",
                        "res_x",
                        "res_y",
                        "res_z"
                    ],
                    "properties": {
                        "unit": {
                            "description": "Units used to describe the resolution. All dimensions are specified in the same unit.",
                            "$ref": "#/definitions/onto_term"
                        },
                        "res_x": {
                            "type": "number",
                            "format": "float"
                        },
                        "res_y": {
                            "type": "number",
                            "format": "float"
                        },
                        "res_z": {
                            "type": "number",
                            "format": "float"
                        }
                    }
                }
            }
        },
        "xref": {
            "description": "Arrays of cross references to external resources.",
            "type": "array",
            "minItems": 1,
            "items": {
                "type": "object",
                "required": [
                    "code",
                    "database"
                ],
                "properties": {
                    "code": {
                        "description": "Cross reference code, for example DOI or PUBMED_ID. The code is used with the database information to build a valid URL.",
                        "type": "string"
                    },
                    "database": {
                        "description": "Reference to an ontology term that contains the needed information to build a valid cross-reference from the code.",
                        "$ref": "#/definitions/onto_term"
                    }
                }
            }
        }
    }
}