bia_mifa_models.schema.json

{
    "$defs": {
        "AnnotationType": {
            "description": "",
            "enum": [
                "class_labels",
                "bounding_boxes",
                "counts",
                "derived_annotations",
                "geometrical_annotations",
                "graphs",
                "point_annotations",
                "segmentation_mask",
                "tracks",
                "weak_annotations",
                "other"
            ],
            "title": "AnnotationType",
            "type": "string"
        },
        "Annotations": {
            "additionalProperties": false,
            "description": "A set of annotations for an AI-ready dataset",
            "properties": {
                "annotation_confidence_level": {
                    "description": "Confidence on annotation accuracy",
                    "type": "string"
                },
                "annotation_coverage": {
                    "description": "Which images from the dataset were annotated, and what percentage of the data has been annotated from what is available",
                    "type": "string"
                },
                "annotation_criteria": {
                    "description": "Rules used to generate annotations",
                    "type": "string"
                },
                "annotation_method": {
                    "description": "Description of how the annotations were created. For example, were the annotations crowdsourced or expertly annotated,  produced by  a human or software, what software was used, when were the annotations created,  protocols used for consensus and quality assurance",
                    "type": "string"
                },
                "annotation_overview": {
                    "description": "Short descriptive summary indicating the type of annotation and how it was generated",
                    "type": "string"
                },
                "authors": {
                    "description": "a collection of the authors of a study",
                    "items": {
                        "$ref": "#/$defs/Author"
                    },
                    "type": "array"
                },
                "file_metadata": {
                    "description": "a collection of the file level metadata for each annotation",
                    "items": {
                        "$ref": "#/$defs/FileLevelMetadata"
                    },
                    "type": "array"
                }
            },
            "required": [
                "annotation_overview",
                "annotation_method"
            ],
            "title": "Annotations",
            "type": "object"
        },
        "Author": {
            "additionalProperties": false,
            "description": "Information about the authors",
            "properties": {
                "author_first_name": {
                    "description": "First name for an author",
                    "type": "string"
                },
                "author_last_name": {
                    "description": "Last name for an author",
                    "type": "string"
                },
                "email": {
                    "description": "Email address of a person",
                    "pattern": "^\\S+@[\\S+\\.]+\\S+",
                    "type": "string"
                },
                "orcid_id": {
                    "description": "A unique identifier for an author",
                    "type": "string"
                },
                "organisation": {
                    "description": "a collection of the name and address of organisations authors are affiliated with",
                    "items": {
                        "$ref": "#/$defs/OrganisationInfo"
                    },
                    "type": "array"
                },
                "role": {
                    "description": "Role of the author when creating the dataset",
                    "items": {
                        "type": "string"
                    },
                    "type": "array"
                }
            },
            "required": [
                "author_first_name",
                "author_last_name"
            ],
            "title": "Author",
            "type": "object"
        },
        "FileLevelMetadata": {
            "additionalProperties": false,
            "description": "metadata atributes that must be detailed at the file level",
            "properties": {
                "annotation_creation_time": {
                    "description": "Date and time when the annotation was created",
                    "format": "date-time",
                    "type": "string"
                },
                "annotation_id": {
                    "description": "The identifier for the annotation",
                    "type": "string"
                },
                "annotation_type": {
                    "description": "Annotation type, for example class labels, segmentation masks, counts...",
                    "items": {
                        "$ref": "#/$defs/AnnotationType"
                    },
                    "type": "array"
                },
                "source_image_id": {
                    "description": "identifier of the source image from which the annotation originated",
                    "type": "string"
                },
                "spatial_information": {
                    "description": "Spatial information for non-pixel annotations",
                    "type": "string"
                },
                "transformations": {
                    "description": "Any transformations required to link the images to the annotations",
                    "type": "string"
                }
            },
            "required": [
                "annotation_id",
                "annotation_type",
                "source_image_id"
            ],
            "title": "FileLevelMetadata",
            "type": "object"
        },
        "GrantReference": {
            "additionalProperties": false,
            "description": "Information about grant ID and funding body that funded the study",
            "properties": {
                "funder": {
                    "description": "The funding body provididing support",
                    "type": "string"
                },
                "grant_id": {
                    "description": "The identifier for the grant",
                    "type": "string"
                }
            },
            "required": [
                "grant_id",
                "funder"
            ],
            "title": "GrantReference",
            "type": "object"
        },
        "LicenseType": {
            "description": "",
            "enum": [
                "CC0",
                "CC_BY"
            ],
            "title": "LicenseType",
            "type": "string"
        },
        "OrganisationInfo": {
            "additionalProperties": false,
            "description": "Information about the organisation the author is affiliated with",
            "properties": {
                "address": {
                    "description": "Organisation address",
                    "type": "string"
                },
                "organisation_name": {
                    "description": "Organisation name",
                    "type": "string"
                },
                "ror_id": {
                    "description": "Identifier for the Research Organization Registry",
                    "type": "string"
                }
            },
            "required": [
                "organisation_name"
            ],
            "title": "OrganisationInfo",
            "type": "object"
        },
        "Publications": {
            "additionalProperties": false,
            "description": "Information about any publications associated with the dataset",
            "properties": {
                "publication_authors": {
                    "description": "Authors of associated publication",
                    "type": "string"
                },
                "publication_doi": {
                    "description": "Digital Object Identifier (DOI)",
                    "type": "string"
                },
                "publication_title": {
                    "description": "The title for a publication associated to the dataset",
                    "type": "string"
                },
                "publication_year": {
                    "description": "Year of publication",
                    "type": "string"
                },
                "pubmed_id": {
                    "description": "Identifier for journal articles/abstracts in PubMed",
                    "type": "string"
                }
            },
            "required": [
                "publication_title",
                "publication_authors",
                "publication_doi"
            ],
            "title": "Publications",
            "type": "object"
        },
        "Publications__identifier_optional": {
            "additionalProperties": false,
            "description": "Information about any publications associated with the dataset",
            "properties": {
                "publication_authors": {
                    "description": "Authors of associated publication",
                    "type": "string"
                },
                "publication_doi": {
                    "description": "Digital Object Identifier (DOI)",
                    "type": "string"
                },
                "publication_title": {
                    "description": "The title for a publication associated to the dataset",
                    "type": "string"
                },
                "publication_year": {
                    "description": "Year of publication",
                    "type": "string"
                },
                "pubmed_id": {
                    "description": "Identifier for journal articles/abstracts in PubMed",
                    "type": "string"
                }
            },
            "required": [
                "publication_title",
                "publication_authors"
            ],
            "title": "Publications",
            "type": "object"
        },
        "Study": {
            "additionalProperties": false,
            "description": "General information about the study",
            "properties": {
                "acknowledgements": {
                    "description": "Any people or groups that should be acknowledged as part of the dataset",
                    "type": "string"
                },
                "ai_models_trained": {
                    "description": "Link to the models that have been trained with this dataset (if any). This could be links to GitHub or repositories like the BioImage Zoo.",
                    "items": {
                        "type": "string"
                    },
                    "type": "array"
                },
                "authors": {
                    "description": "a collection of the authors of a study",
                    "items": {
                        "$ref": "#/$defs/Author"
                    },
                    "type": "array"
                },
                "description": {
                    "description": "Brief description of the detaset. Must contain the biological application of the dataset",
                    "type": "string"
                },
                "funding_statement": {
                    "description": "Description of how the study was funded",
                    "type": "string"
                },
                "grants": {
                    "description": "a collection of grant ids and funder names associated with the study",
                    "items": {
                        "$ref": "#/$defs/GrantReference"
                    },
                    "type": "array"
                },
                "keywords": {
                    "description": "Keywords or tags used to describe the dataset",
                    "items": {
                        "type": "string"
                    },
                    "type": "array"
                },
                "license": {
                    "$ref": "#/$defs/LicenseType",
                    "description": "The license under which the data are available"
                },
                "link_description": {
                    "description": "The description of the linked content",
                    "items": {
                        "type": "string"
                    },
                    "type": "array"
                },
                "link_url": {
                    "description": "URL of relevant link",
                    "items": {
                        "type": "string"
                    },
                    "type": "array"
                },
                "publications": {
                    "additionalProperties": {
                        "$ref": "#/$defs/Publications__identifier_optional"
                    },
                    "description": "a collection of publications associated with a study",
                    "type": "object"
                },
                "title": {
                    "description": "The title for your dataset. This will be displayed when search results including your data are shown. Often this will be the same as an associated publication.",
                    "type": "string"
                }
            },
            "required": [
                "title",
                "description",
                "keywords",
                "license",
                "funding_statement",
                "link_url"
            ],
            "title": "Study",
            "type": "object"
        },
        "Version": {
            "additionalProperties": false,
            "description": "Information about the dataset version",
            "properties": {
                "changes": {
                    "description": "Textual description of changes compared to previous version",
                    "type": "string"
                },
                "previous_version": {
                    "description": "Pointer to previous version",
                    "type": "string"
                },
                "timestamp": {
                    "description": "Date and time when the version was created",
                    "format": "date-time",
                    "type": "string"
                },
                "version": {
                    "description": "Unique version number",
                    "type": "string"
                }
            },
            "required": [
                "version",
                "timestamp"
            ],
            "title": "Version",
            "type": "object"
        }
    },
    "$id": "https://w3id.org/BioImage-Archive/bia-mifa-models",
    "$schema": "http://json-schema.org/draft-07/schema#",
    "additionalProperties": true,
    "description": "A set of annotations for an AI-ready dataset",
    "metamodel_version": "1.7.0",
    "properties": {
        "annotation_confidence_level": {
            "description": "Confidence on annotation accuracy",
            "type": "string"
        },
        "annotation_coverage": {
            "description": "Which images from the dataset were annotated, and what percentage of the data has been annotated from what is available",
            "type": "string"
        },
        "annotation_criteria": {
            "description": "Rules used to generate annotations",
            "type": "string"
        },
        "annotation_method": {
            "description": "Description of how the annotations were created. For example, were the annotations crowdsourced or expertly annotated,  produced by  a human or software, what software was used, when were the annotations created,  protocols used for consensus and quality assurance",
            "type": "string"
        },
        "annotation_overview": {
            "description": "Short descriptive summary indicating the type of annotation and how it was generated",
            "type": "string"
        },
        "authors": {
            "description": "a collection of the authors of a study",
            "items": {
                "$ref": "#/$defs/Author"
            },
            "type": "array"
        },
        "file_metadata": {
            "description": "a collection of the file level metadata for each annotation",
            "items": {
                "$ref": "#/$defs/FileLevelMetadata"
            },
            "type": "array"
        }
    },
    "required": [
        "annotation_overview",
        "annotation_method"
    ],
    "title": "bia-mifa-models",
    "type": "object",
    "version": null
}