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scope-json-metadata.schema.json
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{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "http://github.com/aertslab/SCope/scope-json-metadata.schema",
"title": "SCope metadata",
"description": "The metadata stored in a SCope compatible loom file",
"type": "object",
"properties": {
"embeddings": {
"description": "List of all embeddings stored in the loom file, must contain one entry for -1",
"type": "array",
"items": {
"type": "object",
"minProperties": 1,
"properties": {
"id": {
"type": "integer",
"description": "Index of embeddings matrix in Embeddings_X and Embeddings_Y. -1 is special case and is stored in Embedding",
"minimum": -1
},
"name": {
"type": "string",
"description": "Name shown in SCope"
}
},
"required": ["id", "name"]
}
},
"clusterings": {
"description": "List of all clusterings stored in the loom file. Each element in the array is a different clustering (i.e. Louvain at different resolutions).",
"type": "array",
"items": {
"type": "object",
"properties": {
"id": {
"type": "integer",
"description": "Index of clustering used throughout this loom file",
"minimum": 0
},
"group": {
"type": "string",
"description": "TODO"
},
"name": {
"type": "string",
"description": "Name of clustering displayed in SCope"
},
"clusters": {
"type": "array",
"description": "Array of id -> name links for clusters",
"items": {
"type": "object",
"properties": {
"id": {
"type": "integer",
"description": "Index of cluster within this clustering",
"minimum": 0
},
"description": {
"type": "string",
"description": "Name of the cluster displayed in SCope"
},
"cell_type_annotation": {
"type": "array",
"description": "Possible annotations for the cluster",
"items": {
"type": "object",
"properties": {
"data": {
"type": "object",
"description": "Actual data for the annotation",
"properties": {
"curator_name": {
"type": "string",
"description": "Real name of the curator or tool"
},
"curator_id": {
"type": "string",
"description": "ORCID ID of the curator or version number of the tool"
},
"timestamp": {
"type": "integer",
"description": "timestamp"
},
"obo_id": {
"type": "string",
"description": "Controlled vocabulary term"
},
"ols_iri": {
"type": "string",
"description": "Optional URL linking to vocabulary"
},
"annotation_label": {
"type": "string",
"description": "Vocabulary name or free text annotation"
},
"markers": {
"type": "array",
"description": "markers",
"items": {
"type": "string"
}
},
"publication": {
"type": "string",
"description": "Related publication DOI (Full URL)"
},
"comment": {
"type": "string",
"description": "Free text comment"
}
},
"required": [
"curator_name",
"curator_id",
"timestamp",
"obo_id",
"ols_iri",
"annotation_label",
"markers",
"publication",
"comment"
]
},
"validate_hash": {
"type": "string",
"description": "SHA256 hash of annotation data + salt"
},
"votes": {
"type": "object",
"description": "Vote information for this annotation",
"properties": {
"votes_for": {
"type": "object",
"description": "Data for positive votes",
"properties": {
"total": {
"type": "integer",
"description": "Number of total votes"
},
"voters": {
"type": "array",
"description": "Array of voter information",
"items": {
"type": "object",
"description": "Information about voters",
"properties": {
"voter_name": {
"type": "string",
"description": "Real name of voter"
},
"voter_id": {
"type": "string",
"description": "ORCID ID of voter"
},
"voter_hash": {
"type": "string",
"description": "SHA256 hash of data + ORCID ID + salt"
}
},
"required": ["voter_name", "voter_id", "voter_hash"]
}
}
},
"required": ["voters"]
},
"votes_against": {
"type": "object",
"description": "Data for negative votes",
"properties": {
"total": {
"type": "integer",
"description": "Number of total votes"
},
"voters": {
"type": "array",
"description": "Array of voter information",
"items": {
"type": "object",
"description": "Information about voters",
"properties": {
"voter_name": {
"type": "string",
"description": "Real name of voter"
},
"voter_id": {
"type": "string",
"description": "ORCID ID of voter"
},
"voter_hash": {
"type": "string",
"description": "SHA256 hash of data + ORCID ID + salt"
}
},
"required": ["voter_name", "voter_id", "voter_hash"]
}
}
},
"required": ["voters"]
}
},
"required": ["votes_for", "votes_against"]
}
},
"required": ["data", "validate_hash", "votes"]
}
}
},
"required": ["id", "description"]
}
},
"clusterColors": {
"type": "array",
"description": "A unique set of the colors associated to each cluster",
"items": {
"type": "string"
}
},
"clusterMarkerMetrics": {
"type": "array",
"description": "List of different metrics available from the clustering. Shown in the table in the right sidebar of SCope",
"items": {
"type": "object",
"properties": {
"accessor": {
"type": "string",
"description": "Variable name stored in row attributes"
},
"name": {
"type": "string",
"description": "Name of metric"
},
"description": {
"type": "string",
"description": "Description of metric"
}
},
"required": ["accessor", "name", "description"]
}
}
},
"required": ["id", "name"]
}
},
"regulonThresholds": {
"type": "array",
"description": "List of thresholds generated form SCENIC per regulon",
"items": {
"type": "object",
"properties": {
"regulon": {
"type": "string",
"description": "Name of regulon"
},
"defaultThresholdValue": {
"type": "number",
"minimum": 0,
"description": "Value of the default threshold"
},
"defaultThresholdName": {
"type": "string",
"description": "Name of the default threshold"
},
"allThresholds": {
"type": "object",
"uniqueItems": true,
"additionalProperties": {
"type": "number"
}
},
"motifData": {
"type": "string",
"description": "Filename for the motif logo"
},
"motifVersion": {
"type": "string",
"description": "Version for the motif logo",
"enum": ["V8", "V9"]
}
},
"required": ["regulon", "defaultThresholdName", "defaultThresholdValue"]
}
},
"annotations": {
"type": "array",
"description": "List of annotations visible in scope",
"items": {
"type": "object",
"properties": {
"name": {
"type": "string",
"description": "Name of the annotation"
},
"values": {
"type": "array",
"description": "A unique set of the values of the annotation",
"items": {
"type": "string"
}
},
"colors": {
"type": "array",
"description": "A unique set of the colors associated to each value of the annotation",
"items": {
"type": "string"
}
}
},
"required": ["name", "values"]
}
},
"metrics": {
"type": "array",
"description": "A list of the metrics viewable (column attributes)",
"items": {
"type": "object",
"properties": {
"name": {
"type": "string",
"description": "Name of the column attribute to enable colouring of"
}
},
"required": ["name"]
}
}
},
"required": ["embeddings"]
}