FindSim-Schema.json

{
	"title" : "FindSim schema",
	"description" : "This is a schema for descriptors of experiments used by the FindSim package.",
	"type": "object",
	"properties": {
		"FileType": {"type": "string"},
		"Version": {"type": "string"},
		"Metadata": {
		"type": "object",
			"properties": {
				"transcriber": {"type": "string"},
				"organization": {"type": "string"},
				"email": {"type": "string"},
				"source": {
					"type": "object",
					"properties": {
						"sourceType": {
							"type": "string",
							"enum": ["paper", "inhouse", "database", "simulation", "other"]
						},
						"PMID": {"type": "number"},
						"doi": {"type": "string"},
						"authors": {"type": "string"},
						"journal": {"type": "string"},
						"journalDetail": {"type": "string"},
						"year": {"type": "number"},
						"figure": {"type": "string"},
						"table": {"type": "string"}
					},
					"anyOf": [
						{"required": ["sourceType", "PMID", "year"]},
						{"required": ["sourceType", "doi", "year"]}
					],
					"additionalProperties": false
				},
				"notes": { "type": "string" },
				"testModel": { "type": "string", 
					"description": "This is a reference model against which the findSim expt file should work, typically provided along with it." },
				"testMap": { "type": "string",
			   "description": "Map file to go along with expt file and reference model"	
				}
			},
			"required": ["transcriber", "organization", "source"],
			"additionalProperties": false
		},

		"Experiment": {
			"type": "object",
			"properties": {
				"design": { "type": "string",
					"enum": ["TimeSeries", "DoseResponse", "BarChart", "DirectParameter" ]
			   	},
				"species": { "type": "string" },
				"cellType": { "type": "string" },
				"samplePrep": { "type": "string" },
				"sampleType": { "type": "string" },
				"temperature": { "type": "number" },
				"notes": { "type": "string" }
			},
			"required": ["design"],
			"additionalProperties": false
		},

		"Stimuli":{ "type": "array", 
			"items": {
				"type": "object",
				"properties": {
					"timeUnits": {"type": "string",
						"enum": ["s", "sec", "min", "hr", "day", "ms", "msec", "us", "usec"]
			   		},
					"quantityUnits": {"type": "string",
						"enum": ["nM", "uM", "mM", "M", "#", "uV", "mV", "V", "pA", "nA", "uA", "Hz", "ratio"],
						"description": "Hz is used for synaptic input at a given freq. Ratio comes up for neuromodulation of synaptic weight and channels"
			   		},
					"entity": {"type": "string" },
					"label": {
						"type": "string",
						"description" : "label is used only by BarCharts. It uniquely identifies stimulus blocks. By default the BarChart uses the _entity_ name, but in case there are multiple stimuli involving the same entity the _label_ lets one give each a unique identifier."
					},
					"field": {"type": "string",
						"enum": ["conc", "inject", "Vm", "Vclamp", "rate", "weight","EPSP_peak","synInput"],
						"description": "rate and weight are used for synaptic input"
			   		},
					"isBuffered": {"type": "number" },
					"data": {"type": "array",
						"items": { "type": "array", 
							"items": {"type": "number" },
							"minItems": 2, "maxItems": 2
						}
			   		},
					"value": {"type": "number"}
				},
				"required": ["quantityUnits", "entity", "field"],
				"additionalProperties": false
			}
		},

		"Readouts":{
			"type": "object",
			"properties": {
				"timeUnits": {"type": "string",
					"enum": ["s", "sec", "min", "hr", "day", "ms", "msec", "us", "usec"]
			   	},
				"quantityUnits": {"type": "string",
					"enum": ["nM", "uM", "mM", "M", "#", "uV", "mV", "V", "pA", "nA", "uA", "ratio"]
			   	},
				"entities": {"type": "array",
						"items": {"type": "string"}
				},
				"field": {"type": "string" },
				"window": {"type": "object",
						"properties": {
								"startt": {"type": "number"},
								"endt": {"type": "number"},
								"dt": {"type": "number"},
								"operation": {"type": "string",
									"enum": ["min", "max", "mean", "sdev", "oscPk", "oscVal"]
								}
						},
					"required": ["startt", "endt", "dt", "operation"],
					"additionalProperties": false
				},
				"settleTime": {"type": "number", 
			   		"minimum": 0.0, 
					"maximum": 5000	
				},
				"normalization": {"type": "object",
					"properties": {
						"sampling": {"type": "string",
							"enum": ["none", "start", "end", "min", "max", "each", "presetTime", "dose"]
						},
						"time": {"type": "number"},
						"dose": {"type": "number"},
						"entities": {"type": "array",
							"items": {"type": "string"},
							"minitems":1,
							"description": "If the entities here are different from the primary readout entities, it is a ratio calculation. If they are the same, it is a normalization."
						}
					},
					"required": ["sampling", "entities"],
					"additionalProperties": false
				},
				"display": {"type": "object",
					"properties": {
						"useXlog": {"type": "boolean"},
						"useYlog": {"type": "boolean"},
						"plotDt": {"type": "number", "minimum": 1e-6}
					},
					"additionalProperties": false
				},
				"epsp": {"type": "object",
					"description": "Params to define field recordings",
					"properties": {
						"epspFreq": {"type": "number", "minumum": 0},
						"epspWindow": {"type": "number", 
							"minimum": 1e-6,
							"description": "Time window to search for peak."
						},
						"electrodePosition": {"type": "array",
							"items": {"type": "number" },
							"minItems": 2, "maxItems": 3,
							"description": "position of recording electrode"
						},
						"epspDepthIntegMin": {"type": "number" },
						"epspDepthIntegMax": {"type": "number" }
					},
					"additionalProperties": false
				},
				"data": {"type": "array",
					"items": { "type": "array", 
						"items": {"type": "number" },
						"minItems": 2, "maxItems": 3
					}
			   	},
				"bardata": {"type": "array",
					"items": { "type": "object", 
						"properties": {
							"stimulus": {"type": "array",
								"items": {"type": "string"}
							},
							"value": {"type": "number" },
							"stderr": {"type": "number" }
						},
						"required": ["stimulus", "value", "stderr"]
					},
					"minItems": 1
				},
				"paramdata": {"type": "array",
					"items": { "type": "object", 
						"properties": {
							"entity": {"type": "string"},
							"field": {"type": "string"},
							"units": {"type": "string",
								"enum": ["nM", "uM", "mM", "M", "#", "s", "sec", "1/s", "1/sec", "uV", "mV", "V", "pA", "nA", "uA"]
							},
							"value": {"type": "number" },
							"stderr": {"type": "number" }
						},
						"required": ["entity", "field", "units", "value"],
						"additionalProperties": false
					},
					"minItems": 1
				}
		   	},
			"oneOf": [
				{ "required": ["timeUnits", "quantityUnits", "entities", "field", "data"]}, 
				{ "required": ["timeUnits", "quantityUnits", "entities", "field", "bardata"]},
				{ "required": ["paramdata"]} 
			],
			"additionalProperties": false
		},

		"Modifications":{
			"type": "object",
			"properties": {
				"subset": {"type": "array",
					"items": {"type": "string"}
				},
				"itemsToDelete": {"type": "array",
					"items": {"type": "string"}
				},
				"parameterChange": {"type": "array",
					"items": {"type": "object",
						"properties": {
							"enitity": {"type": "string" },
							"field": {"type": "string" },
							"value": {"type": "number" },
							"units": {"type": "string",
								"enum": ["nM", "uM", "mM", "M", "#", "s", "sec", "1/s", "1/sec", "uV", "mV", "V", "pA", "nA", "uA", "none"]
						   	}
						},
						"required": ["entity", "field", "value", "units"]
					}
				},
				"notes": {"type": "string" }
			},
			"anyOf": [
				{ "required": ["subset"] },
				{ "required": ["itemsToDelete"] },
				{ "required": ["parameterChange"] }
			],
			"additionalProperties": false
		}
	},
	"required": ["Metadata", "Experiment", "Readouts"],
	"additionalProperties": false
}