<commit_before>{
    "title": "Biosample",
    "description": "Schema for submitting a biosample.",
    "id": "/profiles/biosample.json",
    "$schema": "http://json-schema.org/draft-04/schema#",
    "type": "object",
    "required": [ "award", "lab", "biosample_type", "source", "organism", "biosample_term_id"],
    "identifyingProperties": ["uuid","accesion","aliases"],
    "additionalProperties": false,
    "mixinProperties": [
        { "$ref": "mixins.json#/schema_version" },
        { "$ref": "mixins.json#/uuid" },
        { "$ref": "mixins.json#/accession" },
        { "$ref": "mixins.json#/biosample_classification" },
        { "$ref": "mixins.json#/aliases" },
        { "$ref": "mixins.json#/attribution" },
        { "$ref": "mixins.json#/standard_status" },
        { "$ref": "mixins.json#/submitted" },
        { "$ref": "mixins.json#/product_id" },
        { "$ref": "mixins.json#/lot_id" },
        { "$ref": "mixins.json#/source" }
    ],
    "properties": {
        "schema_version": {
            "default": "1"
        },
        "description": {
            "title": "Description",
            "description": "A plain text description of the biosample. Do not include experiment details, constructs or treatments.",
            "type": "string",
            "default": ""
        },
       "constructs": {
            "title": "DNA Constructs",
            "description": "Expression or targeting vectors stably or transiently transfected (not RNAi).",
            "type": "array",
            "default": [],
            "items": {
                "title": "DNA Constructs",
                "description": "An expression or targeting vector stably or transiently transfected (not RNAi).",
                "comment": "See contstruct.json for available identifiers.",
                "type":  "string",
                "linkTo": "construct"
            }
        },
        "rnais": {
            "title": "RNAi Vectors",
            "description": "RNAi vectors stably or transiently transfected.",
            "type": "array",
            "default": [],
            "items": {
                "title": "RNAi Vector",
                "description": "RNAi vector stably or transiently transfected.",
                "comment": "See rnai.json for available identifers.",
                "type":  "string",
                "linkTo": "rnai"
            }
        },
        "treatments": {
            "title": "Treatments",
            "type": "array",
	"default": [],
            "items": {
                "title": "Treatment",
                "comment": "See treatment.json for available identifers.",
	    "type": "string",
                "linkTo": "treatment"
            }
        },
        "encode2_dbxrefs": {
            "title": "Previous ENCODE IDs",
            "type": "array",
            "default": [],
            "items": {
                "title": "Previous ENCODE ID",
                "type":  "string"
            }
        },
        "protocol_documents": {
            "title": "Protocol Documents",
            "description": "Documents that describe the biosample preparation.",
            "type": "array",
            "default": [],
            "items": {
                "title": "Protocol Document",
                "description": "A document that describes the biosample preparation.",
                "comment": "See document.json for available identifiers.",
                "type": "string",
                "linkTo": "document"
            }
        },
        "donor": {
            "title": "Donor",
            "comment": "For human biosamples, see human_donor.json for available identifiers. For mouse biosamples, see mouse_donor.json for available identifiers.",
            "type": "string",
            "linkTo": "donor"
        },
        "organism": {
            "title": "Organism",
            "comment": "See organism.json for available identifiers.",
            "type": "string",
            "linkTo": "organism"
        },
        "passage_number": {
            "title": "Passage Number",
	"description": "In calculating passage number, include passages from the source.",
            "type": "integer"
        },
        "derived_from": {
            "title": "Derived from",
            "description": "The biosamples from which the sample derives from via constructs or treatments.",
            "type":  "array",
            "default": [],
            "items": {
                "description": "A biosample that the sample derives from via a construct or treatment.",
                "comment": "See biosample.json for available identifiers.",
                "type": "string",
                "linkTo": "biosample"
            }
        },
        "pooled_from": {
            "title": "Pooled from",
            "description": "The biosamples from which aliquots were pooled to form the biosample.",
            "type":  "array",
            "default": [],
            "items": {
                "description": "A biosample from which an aliquot was taken to form the biosample.",
                "comment": "See biosample.json for available identifiers.",
                "type": "string",
                "linkTo": "biosample"
            }
        },
        "part_of": {
            "title": "Separated from",
            "description": "The biosamples from which a discrete component were taken. That component is this biosample.",
            "type":  "array",
            "default": [],
            "items": {
                "description": "A biosample from which a discrete component was taken. That component is this biosample.",
                "comment": "See biosamples.json for available identifiers.",
                "type": "string",
                "linkTo": "biosample"
            }
        },
        "note": {
            "title": "Note",
            "description": "Additional information pertaining to the biosample.",
            "type": "string"
        },
        "subcellular_fraction": {
            "title": "Subcellular Fraction",
            "description": "The cellular component that constitutes the biosample.",
            "type": "string",
            "enum": ["nucleus", "cytosol"]
        },
        "phase": {
            "title": "Cell-cycle phase",
            "type": "string",
            "enum": [
                "G1",
                "G1b",
                "G2",
                "S1",
                "S2",
                "S3",
                "S4"
            ]
        },
        "transfection_type": {
            "title": "Transfection Type",
            "description": "The persistence of the transfection construct.",
            "type": "string",
            "enum": [
                "stable", "transient"
            ]
        },
        "culture_harvest_date": {
            "title": "Culture Harvest Date",
	    "description": "For cultured samples, the date the biosample was taken.",
            "type": "string",
            "format": "date"
        },
        "culture_start_date": {
            "title": "Culture Start Date",
	    "description": "For cultured samples, the date the culture was started.",
            "type": "string",
            "format": "date"
        },
        "date_obtained": {
            "title": "Date Obtained",
	    "description": "For tissue samples, the date the biosample was taken.",
            "type": "string",
            "format": "date"
        },
        "starting_amount": {
            "title": "Starting Amount",
            "description": "The initial quantity of cells or tissue obtained.",
            "type": "string"
        },
        "starting_amount_units": {
            "title": "Starting Amount Units",
            "type": "string",
            "enum": [
                "g","mg","cells/ml","cells", "whole embryos", "items", "μg"
            ]
        },
        "url": {
            "title": "URL",
            "description": "An external resource with additional information about the biosample.",
            "type": "string",
            "format": "uri"
        },
        "life_stage": {
            "title": "Life stage",
            "type": "string",
            "enum": [
                "fetal",
                "newborn",
                "child",
                "adult",
                "unknown",
                "embryonic",
                "postnatal"
            ]
        },
        "age": {
            "title": "Age",
            "description": " The age or age range of the donor organism when biological material was sampled.",
            "type": "string",
            "pattern": "^\\d+(\\.\\d+)?(\\-\\d+(\\.\\d+)?)?$"
        },
        "age_units": {
            "title": "Age Units",
            "type": "string",
            "enum": [
                "day",
                "week",
                "month",
                "year"
            ]
        },
        "health_status": {
            "title": "Health Status",
            "type": "string"
        }
    }
}<commit_msg>Fixed spelling errors.<commit_after>{
    "title": "Biosample",
    "description": "Schema for submitting a biosample.",
    "id": "/profiles/biosample.json",
    "$schema": "http://json-schema.org/draft-04/schema#",
    "type": "object",
    "required": [ "award", "lab", "biosample_type", "source", "organism", "biosample_term_id"],
    "identifyingProperties": ["uuid","accesion","aliases"],
    "additionalProperties": false,
    "mixinProperties": [
        { "$ref": "mixins.json#/schema_version" },
        { "$ref": "mixins.json#/uuid" },
        { "$ref": "mixins.json#/accession" },
        { "$ref": "mixins.json#/biosample_classification" },
        { "$ref": "mixins.json#/aliases" },
        { "$ref": "mixins.json#/attribution" },
        { "$ref": "mixins.json#/standard_status" },
        { "$ref": "mixins.json#/submitted" },
        { "$ref": "mixins.json#/product_id" },
        { "$ref": "mixins.json#/lot_id" },
        { "$ref": "mixins.json#/source" }
    ],
    "properties": {
        "schema_version": {
            "default": "1"
        },
        "description": {
            "title": "Description",
            "description": "A plain text description of the biosample. Do not include experiment details, constructs or treatments.",
            "type": "string",
            "default": ""
        },
       "constructs": {
            "title": "DNA Constructs",
            "description": "Expression or targeting vectors stably or transiently transfected (not RNAi).",
            "type": "array",
            "default": [],
            "items": {
                "title": "DNA Constructs",
                "description": "An expression or targeting vector stably or transiently transfected (not RNAi).",
                "comment": "See contstruct.json for available identifiers.",
                "type":  "string",
                "linkTo": "construct"
            }
        },
        "rnais": {
            "title": "RNAi Vectors",
            "description": "RNAi vectors stably or transiently transfected.",
            "type": "array",
            "default": [],
            "items": {
                "title": "RNAi Vector",
                "description": "RNAi vector stably or transiently transfected.",
                "comment": "See rnai.json for available identifiers.",
                "type":  "string",
                "linkTo": "rnai"
            }
        },
        "treatments": {
            "title": "Treatments",
            "type": "array",
	"default": [],
            "items": {
                "title": "Treatment",
                "comment": "See treatment.json for available identifiers.",
	    "type": "string",
                "linkTo": "treatment"
            }
        },
        "encode2_dbxrefs": {
            "title": "Previous ENCODE IDs",
            "type": "array",
            "default": [],
            "items": {
                "title": "Previous ENCODE ID",
                "type":  "string"
            }
        },
        "protocol_documents": {
            "title": "Protocol Documents",
            "description": "Documents that describe the biosample preparation.",
            "type": "array",
            "default": [],
            "items": {
                "title": "Protocol Document",
                "description": "A document that describes the biosample preparation.",
                "comment": "See document.json for available identifiers.",
                "type": "string",
                "linkTo": "document"
            }
        },
        "donor": {
            "title": "Donor",
            "comment": "For human biosamples, see human_donor.json for available identifiers. For mouse biosamples, see mouse_donor.json for available identifiers.",
            "type": "string",
            "linkTo": "donor"
        },
        "organism": {
            "title": "Organism",
            "comment": "See organism.json for available identifiers.",
            "type": "string",
            "linkTo": "organism"
        },
        "passage_number": {
            "title": "Passage Number",
	"description": "In calculating passage number, include passages from the source.",
            "type": "integer"
        },
        "derived_from": {
            "title": "Derived from",
            "description": "The biosamples from which the sample derives from via constructs or treatments.",
            "type":  "array",
            "default": [],
            "items": {
                "description": "A biosample that the sample derives from via a construct or treatment.",
                "comment": "See biosample.json for available identifiers.",
                "type": "string",
                "linkTo": "biosample"
            }
        },
        "pooled_from": {
            "title": "Pooled from",
            "description": "The biosamples from which aliquots were pooled to form the biosample.",
            "type":  "array",
            "default": [],
            "items": {
                "description": "A biosample from which an aliquot was taken to form the biosample.",
                "comment": "See biosample.json for available identifiers.",
                "type": "string",
                "linkTo": "biosample"
            }
        },
        "part_of": {
            "title": "Separated from",
            "description": "The biosamples from which a discrete component were taken. That component is this biosample.",
            "type":  "array",
            "default": [],
            "items": {
                "description": "A biosample from which a discrete component was taken. That component is this biosample.",
                "comment": "See biosamples.json for available identifiers.",
                "type": "string",
                "linkTo": "biosample"
            }
        },
        "note": {
            "title": "Note",
            "description": "Additional information pertaining to the biosample.",
            "type": "string"
        },
        "subcellular_fraction": {
            "title": "Subcellular Fraction",
            "description": "The cellular component that constitutes the biosample.",
            "type": "string",
            "enum": ["nucleus", "cytosol"]
        },
        "phase": {
            "title": "Cell-cycle phase",
            "type": "string",
            "enum": [
                "G1",
                "G1b",
                "G2",
                "S1",
                "S2",
                "S3",
                "S4"
            ]
        },
        "transfection_type": {
            "title": "Transfection Type",
            "description": "The persistence of the transfection construct.",
            "type": "string",
            "enum": [
                "stable", "transient"
            ]
        },
        "culture_harvest_date": {
            "title": "Culture Harvest Date",
	    "description": "For cultured samples, the date the biosample was taken.",
            "type": "string",
            "format": "date"
        },
        "culture_start_date": {
            "title": "Culture Start Date",
	    "description": "For cultured samples, the date the culture was started.",
            "type": "string",
            "format": "date"
        },
        "date_obtained": {
            "title": "Date Obtained",
	    "description": "For tissue samples, the date the biosample was taken.",
            "type": "string",
            "format": "date"
        },
        "starting_amount": {
            "title": "Starting Amount",
            "description": "The initial quantity of cells or tissue obtained.",
            "type": "string"
        },
        "starting_amount_units": {
            "title": "Starting Amount Units",
            "type": "string",
            "enum": [
                "g","mg","cells/ml","cells", "whole embryos", "items", "μg"
            ]
        },
        "url": {
            "title": "URL",
            "description": "An external resource with additional information about the biosample.",
            "type": "string",
            "format": "uri"
        },
        "life_stage": {
            "title": "Life stage",
            "type": "string",
            "enum": [
                "fetal",
                "newborn",
                "child",
                "adult",
                "unknown",
                "embryonic",
                "postnatal"
            ]
        },
        "age": {
            "title": "Age",
            "description": " The age or age range of the donor organism when biological material was sampled.",
            "type": "string",
            "pattern": "^\\d+(\\.\\d+)?(\\-\\d+(\\.\\d+)?)?$"
        },
        "age_units": {
            "title": "Age Units",
            "type": "string",
            "enum": [
                "day",
                "week",
                "month",
                "year"
            ]
        },
        "health_status": {
            "title": "Health Status",
            "type": "string"
        }
    }
}
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