Biosample

Schema for submitting a biosample.

{
    "title": "Biosample",
    "description": "Schema for submitting a biosample.",
    "comment": "For cultured samples this object represents unique growths or culture harvests.",
    "id": "/profiles/biosample.json",
    "$schema": "http://json-schema.org/draft-04/schema#",
    "type": "object",
    "required": [
        "award",
        "lab",
        "biosample_type",
        "source",
        "organism",
        "biosample_term_id",
        "biosample_term_name"
    ],
    "identifyingProperties": [
        "uuid",
        "accession",
        "aliases"
    ],
    "additionalProperties": false,
    "mixinProperties": [
        {
            "$ref": "mixins.json#/genetic_modifications"
        },
        {
            "$ref": "mixins.json#/biosample_classification"
        },
        {
            "$ref": "mixins.json#/product_id"
        },
        {
            "$ref": "mixins.json#/lot_id"
        },
        {
            "$ref": "mixins.json#/source"
        },
        {
            "$ref": "mixins.json#/references"
        },
        {
            "$ref": "mixins.json#/documents"
        },
        {
            "$ref": "mixins.json#/submitter_comment"
        },
        {
            "$ref": "mixins.json#/notes"
        },
        {
            "$ref": "mixins.json#/submitted"
        },
        {
            "$ref": "mixins.json#/attribution"
        },
        {
            "$ref": "mixins.json#/accessioned_status"
        },
        {
            "$ref": "mixins.json#/schema_version"
        },
        {
            "$ref": "mixins.json#/aliases"
        },
        {
            "$ref": "mixins.json#/accession"
        },
        {
            "$ref": "mixins.json#/uuid"
        }
    ],
    "dependencies": {
        "phase": {
            "comment": "The phase property is restricted to biosamples with biosample_type that belongs to [primary cell, immortalized cell line, in vitro differentiated cells, induced pluripotent stem cell line, stem cell].",
            "properties": {
                "biosample_type": {
                    "enum": [
                        "primary cell",
                        "immortalized cell line",
                        "in vitro differentiated cells",
                        "stem cell",
                        "induced pluripotent stem cell line"
                    ]
                }
            }
        },
        "rnais": {
            "comment": "RNAi transfected biosamples require specification of the transfection_type.",
            "oneOf": [
                {
                    "required": [
                        "transfection_type"
                    ],
                    "properties": {
                        "rnais": {
                            "minItems": 1
                        }
                    }
                },
                {
                    "properties": {
                        "rnais": {
                            "maxItems": 0
                        }
                    }
                }
            ]
        },
        "constructs": {
            "comment": "Transfected biosamples require specification of the transfection_type.",
            "oneOf": [
                {
                    "required": [
                        "transfection_type"
                    ],
                    "properties": {
                        "constructs": {
                            "minItems": 1
                        }
                    }
                },
                {
                    "properties": {
                        "constructs": {
                            "maxItems": 0
                        }
                    }
                }
            ]
        },
        "transfection_method": {
            "required": [
                "transfection_type"
            ],
            "comment": "Transfected biosamples require specification of the transfection_type."
        },
        "biosample_term_id": {
            "oneOf": [
                {
                    "properties": {
                        "biosample_type": {
                            "enum": [
                                "tissue",
                                "whole organisms"
                            ]
                        },
                        "biosample_term_id": {
                            "pattern": "^(UBERON|NTR):[0-9]{2,8}$"
                        }
                    }
                },
                {
                    "properties": {
                        "biosample_type": {
                            "enum": [
                                "primary cell"
                            ]
                        },
                        "biosample_term_id": {
                            "pattern": "^(CL|NTR):[0-9]{2,8}$"
                        }
                    }
                },
                {
                    "properties": {
                        "biosample_type": {
                            "enum": [
                                "immortalized cell line",
                                "induced pluripotent stem cell line"
                            ]
                        },
                        "biosample_term_id": {
                            "pattern": "^(EFO|NTR):[0-9]{2,8}$"
                        }
                    }
                },
                {
                    "properties": {
                        "biosample_type": {
                            "enum": [
                                "stem cell",
                                "in vitro differentiated cells"
                            ]
                        },
                        "biosample_term_id": {
                            "pattern": "^(CL|EFO|NTR):[0-9]{2,8}$"
                        }
                    }
                }
            ]
        },
        "biosample_type": {
            "not": {
                "properties": {
                    "biosample_type": {
                        "enum": [
                            "whole organisms"
                        ]
                    },
                    "organism": {
                        "linkTo": "Organism",
                        "linkEnum": [
                            "7745b647-ff15-4ff3-9ced-b897d4e2983c"
                        ]
                    }
                }
            }
        },
        "post_synchronization_time_units": {
            "comment": "Biosample with a specified post_synchronization_units requires post_synchronization_time specification and specification of the model organism synchronization stage.",
            "allOf": [
                {
                    "not": {
                        "properties": {
                            "organism": {
                                "linkTo": "Organism",
                                "linkEnum": [
                                    "7745b647-ff15-4ff3-9ced-b897d4e2983c",
                                    "3413218c-3d86-498b-a0a2-9a406638e786"
                                ]
                            }
                        }
                    }
                },
                {
                    "oneOf": [
                        {
                            "required": [
                                "fly_synchronization_stage",
                                "post_synchronization_time"
                            ]
                        },
                        {
                            "required": [
                                "worm_synchronization_stage",
                                "post_synchronization_time"
                            ]
                        }
                    ]
                }
            ]
        },
        "post_treatment_time": {
            "required": [
                "post_treatment_time_units",
                "treatments"
            ],
            "comment": "Biosample with a specified post_treatment_time requires non-empty treatments list and post_treatment_time_units specification.",
            "properties": {
                "treatments": {
                    "minItems": 1
                }
            }
        },
        "post_treatment_time_units": {
            "required": [
                "post_treatment_time",
                "treatments"
            ],
            "comment": "Biosample with a specified post_treatment_time_units requires requires non-empty treatments list post_treatment_time specification.",
            "properties": {
                "treatments": {
                    "minItems": 1
                }
            }
        },
        "pooled_from": {
            "comment": "Biosample with a specified pooled_from list requires at least two entries in the list.",
            "properties": {
                "pooled_from": {
                    "minItems": 2
                }
            }
        },
        "culture_harvest_date": {
            "comment": "The culture_harvest_date property is restricted to biosamples with biosample_type that belongs to [primary cell, immortalized cell line, in vitro differentiated cells, induced pluripotent stem cell line, stem cell].",
            "properties": {
                "biosample_type": {
                    "enum": [
                        "tissue",
                        "primary cell",
                        "immortalized cell line",
                        "in vitro differentiated cells",
                        "stem cell",
                        "induced pluripotent stem cell line"
                    ]
                }
            }
        },
        "culture_start_date": {
            "comment": "The culture_start_date property is restricted to biosamples with biosample_type that belongs to [primary cell, immortalized cell line, in vitro differentiated cells, induced pluripotent stem cell line, stem cell].",
            "properties": {
                "biosample_type": {
                    "enum": [
                        "tissue",
                        "primary cell",
                        "immortalized cell line",
                        "in vitro differentiated cells",
                        "stem cell",
                        "induced pluripotent stem cell line"
                    ]
                }
            }
        },
        "starting_amount": {
            "required": [
                "starting_amount_units"
            ],
            "comment": "Biosample with a specified starting_amount requires starting_amount_units specification."
        },
        "starting_amount_units": {
            "required": [
                "starting_amount"
            ],
            "comment": "Biosample with a specified starting_amount_units requires starting_amount specification."
        },
        "model_organism_age_units": {
            "required": [
                "model_organism_age"
            ],
            "comment": "Biosample with a specified model_organism_age_units requires model_organism_age specification."
        },
        "depleted_in_term_name": {
            "comment": "Only biosamples with biosample_type whole organisms or tissue are allowed to have depleted_in_term_name property.",
            "properties": {
                "biosample_type": {
                    "enum": [
                        "whole organisms",
                        "tissue"
                    ]
                }
            }
        },
        "model_organism_age": {
            "comment": "Biosample with a specified model_organism_age requires model_organism_age_units specification.",
            "required": [
                "model_organism_age_units"
            ]
        },
        "model_organism_mating_status": {
            "comment": "Biosample with a specified model_organism_mating_status requires model_organism_sex specification.",
            "required": [
                "model_organism_sex"
            ]
        },
        "organism": {
            "comment": "Human biosamples are not allowed to have model organism properties, and biosample_type should be different from whole organisms.",
            "oneOf": [
                {
                    "not": {
                        "properties": {
                            "organism": {
                                "linkTo": "Organism",
                                "linkEnum": [
                                    "7745b647-ff15-4ff3-9ced-b897d4e2983c"
                                ]
                            }
                        }
                    }
                },
                {
                    "allOf": [
                        {
                            "properties": {
                                "biosample_type": {
                                    "enum": [
                                        "primary cell",
                                        "immortalized cell line",
                                        "tissue",
                                        "in vitro differentiated cells",
                                        "induced pluripotent stem cell line",
                                        "stem cell"
                                    ]
                                },
                                "organism": {
                                    "linkTo": "Organism",
                                    "linkEnum": [
                                        "7745b647-ff15-4ff3-9ced-b897d4e2983c"
                                    ]
                                }
                            }
                        },
                        {
                            "not": {
                                "required": [
                                    "model_organism_mating_status"
                                ]
                            }
                        },
                        {
                            "not": {
                                "required": [
                                    "model_organism_sex"
                                ]
                            }
                        },
                        {
                            "not": {
                                "required": [
                                    "model_organism_health_status"
                                ]
                            }
                        },
                        {
                            "not": {
                                "required": [
                                    "model_organism_age"
                                ]
                            }
                        }
                    ]
                }
            ]
        },
        "post_synchronization_time": {
            "comment": "Human and mouse biosamples are not allowed to have post_synchronization_time property. Biosample with a specified post_synchronization_time requires post_synchronization_time_units specification and model organism synchronization stage.",
            "allOf": [
                {
                    "not": {
                        "properties": {
                            "organism": {
                                "linkTo": "Organism",
                                "linkEnum": [
                                    "7745b647-ff15-4ff3-9ced-b897d4e2983c",
                                    "3413218c-3d86-498b-a0a2-9a406638e786"
                                ]
                            }
                        }
                    }
                },
                {
                    "oneOf": [
                        {
                            "required": [
                                "fly_synchronization_stage",
                                "post_synchronization_time_units"
                            ]
                        },
                        {
                            "required": [
                                "worm_synchronization_stage",
                                "post_synchronization_time_units"
                            ]
                        }
                    ]
                }
            ]
        },
        "fly_life_stage": {
            "comment": "Only fly biosamples are allowed to have fly_life_stage property.",
            "properties": {
                "organism": {
                    "linkTo": "Organism",
                    "linkEnum": [
                        "ab546d43-8e2a-4567-8db7-a217e6d6eea0",
                        "5be68469-94ba-4d60-b361-dde8958399ca",
                        "74144f1f-f3a6-42b9-abfd-186a1ca93198",
                        "c3cc08b7-7814-4cae-a363-a16b76883e3f",
                        "d1072fd2-8374-4f9b-85ce-8bc2c61de122",
                        "b9ce90a4-b791-40e9-9b4d-ffb1c6a5aa2b",
                        "0bdd955a-57f0-4e4b-b93d-6dd1df9b766c"
                    ]
                }
            }
        },
        "fly_synchronization_stage": {
            "comment": "Only fly biosamples are allowed to have fly_synchronization_stage property.",
            "properties": {
                "organism": {
                    "linkTo": "Organism",
                    "linkEnum": [
                        "ab546d43-8e2a-4567-8db7-a217e6d6eea0",
                        "5be68469-94ba-4d60-b361-dde8958399ca",
                        "74144f1f-f3a6-42b9-abfd-186a1ca93198",
                        "c3cc08b7-7814-4cae-a363-a16b76883e3f",
                        "d1072fd2-8374-4f9b-85ce-8bc2c61de122",
                        "b9ce90a4-b791-40e9-9b4d-ffb1c6a5aa2b",
                        "0bdd955a-57f0-4e4b-b93d-6dd1df9b766c"
                    ]
                }
            }
        },
        "worm_synchronization_stage": {
            "comment": "Only roundworm biosamples are allowed to have worm_synchronization_stage property.",
            "properties": {
                "organism": {
                    "linkTo": "Organism",
                    "linkEnum": [
                        "2732dfd9-4fe6-4fd2-9d88-61b7c58cbe20",
                        "e3ec4c1b-a203-4fe7-a013-96c2d45ab242",
                        "69efae2b-4df5-4957-81da-346f1b93cb98",
                        "a7e711b9-534c-44a3-a782-2a15af620739",
                        "451f9e49-685d-40d5-ad89-760b2512262a"
                    ]
                }
            }
        },
        "worm_life_stage": {
            "comment": "Only roundworm biosamples are allowed to have worm_life_stage property.",
            "properties": {
                "organism": {
                    "linkTo": "Organism",
                    "linkEnum": [
                        "2732dfd9-4fe6-4fd2-9d88-61b7c58cbe20",
                        "e3ec4c1b-a203-4fe7-a013-96c2d45ab242",
                        "69efae2b-4df5-4957-81da-346f1b93cb98",
                        "a7e711b9-534c-44a3-a782-2a15af620739",
                        "451f9e49-685d-40d5-ad89-760b2512262a"
                    ]
                }
            }
        },
        "mouse_life_stage": {
            "comment": "Only mouse biosamples are allowed to have mouse_life_stage property.",
            "properties": {
                "organism": {
                    "linkTo": "Organism",
                    "linkEnum": [
                        "3413218c-3d86-498b-a0a2-9a406638e786"
                    ]
                }
            }
        }
    },
    "properties": {
        "uuid": {
            "description": "The unique identifier associated with every object.",
            "format": "uuid",
            "readonly": true,
            "title": "UUID",
            "serverDefault": "uuid4",
            "requestMethod": "POST",
            "type": "string",
            "comment": "Do not submit. The uuid is set by the server.",
            "permission": "import_items"
        },
        "accession": {
            "description": "A unique identifier to be used to reference the object prefixed with ENC.",
            "format": "accession",
            "readonly": true,
            "accessionType": "BS",
            "serverDefault": "accession",
            "title": "Accession",
            "type": "string",
            "comment": "Do not submit. The accession is assigned by the server.",
            "permission": "import_items"
        },
        "aliases": {
            "title": "Lab aliases",
            "description": "Lab specific identifiers to reference an object.",
            "default": [],
            "uniqueItems": true,
            "type": "array",
            "comment": "The purpose of this field is to provide a link into the lab LIMS and to facilitate shared objects.",
            "items": {
                "description": "A lab specific identifier to reference an object.",
                "uniqueKey": "alias",
                "title": "Lab alias",
                "type": "string",
                "comment": "Current convention is colon separated lab name and lab identifier. (e.g. john-doe:42).",
                "pattern": "^(?:alexander-hoffmann|alexander-rudensky|alexander-urban|ali-mortazavi|alkes-price|andrew-fire|anshul-kundaje|anton-valouev|barbara-wold|bill-noble|bin-yu|bing-ren|bradley-bernstein|brenton-graveley|chris-burge|christina-leslie|colin-dewey|david-gifford|david-gilbert|douglas-black|elliott-margulies|emery-bresnick|encode-awg|encode-consortium|encode-processing-pipeline|erez-lieberman|eric-lecuyer|eric-mendehall|ewan-birney|feng-yue|gene-yeo|george-stamatoyannopoulos|greg-cooper|gregory-crawford|guo-cheng-yuan|haiyan-huang|howard-chang|j-michael-cherry|jason-ernst|jason-lieb|jennifer-harrow|jeremy-luban|job-dekker|joe-ecker|john-lis|john-rinn|john-stamatoyannopoulos|jonathan-pritchard|joseph-costello|kenneth-offit|kevin-struhl|kevin-white|ladeana-hillier|laura-elnitski|len-pennacchio|leonard-lipovich|manolis-kellis|manuel-garber|mark-gerstein|mats-ljungman|matteo-pellegrini|michael-beer|michael-hoffman|michael-snyder|morgan-giddings|nadav-ahituv|paul-khavari|peggy-farnham|peter-bickel|peter-park|piero-carninci|rafael-irizarry|richard-myers|roadmap-epigenomics|robert-klein|robert-waterston|roderic-guigo|ross-hardison|scott-tenenbaum|sherman-weissman|souma-raychaudhuri|stephen-smale|sunduz-keles|susan-celniker|thomas-gingeras|thomas-tullius|tim-reddy|timothy-hubbard|ting-wang|tommi-jaakkola|unknown|valerie-reinke|vishwanath-iyer|w-james-kent|wei-wang|will-greenleaf|xiang-dong-fu|xiaole-shirley|xinshu-xiao|yi-xing|yijun-ruan|yin-shen|yoav-gilad|zhiping-weng|brian-oliver|david-macalpine|hugo-bellen|peter-cherbas|terry-orr-weaver|abby-dernburg|anthony-hyman|arshad-desai|david-miller|eric-lai|fabio-piano|frank-slack|gary-karpen|gregory-hannon|james-posakony|john-kim|julie-ahringer|kamran-ahmad|kris-gunsalus|lincoln-stein|michael-brent|michael-maccoss|mitzi-kuroda|nikolaus-rajewsky|norbert-perrimon|philip-green|sarah-elgin|steven-henikoff|steven-russell|susan-strome|vincenzo-pirrotta|MitaniLab|UofC-HGAC|wesley-hung|encode|modern|dnanexus|modencode|gencode|ggr|cgc|bloomington|dssc|kyoto|gtex|pgp|biochain|promocell|nichd):[a-zA-Z\\d_$.+!*,()'-]+(?:\\s[a-zA-Z\\d_$.+!*,()'-]+)*$"
            }
        },
        "schema_version": {
            "title": "Schema Version",
            "description": "The version of the JSON schema that the server uses to validate the object.",
            "default": "18",
            "requestMethod": [],
            "type": "string",
            "comment": "Do not submit. The version used to validate the object is set by the server. The default should be set to the current version.",
            "pattern": "^\\d+(\\.\\d+)*$"
        },
        "status": {
            "description": "The status of the metadata object.",
            "default": "in progress",
            "title": "Status",
            "enum": [
                "in progress",
                "deleted",
                "replaced",
                "released",
                "revoked"
            ],
            "readonly": true,
            "type": "string",
            "comment": "Do not submit.  This is set by admins along the process of metadata submission.",
            "permission": "import_items"
        },
        "lab": {
            "description": "Lab associated with the submission.",
            "linkTo": "Lab",
            "title": "Lab",
            "type": "string",
            "comment": "Required. See lab.json for list of available identifiers.",
            "linkSubmitsFor": true
        },
        "award": {
            "description": "Grant associated with the submission.",
            "type": "string",
            "comment": "Required. See award.json for list of available identifiers.",
            "linkTo": "Award",
            "title": "Grant"
        },
        "date_created": {
            "description": "The date the object was created.",
            "readonly": true,
            "rdfs:subPropertyOf": "dc:created",
            "anyOf": [
                {
                    "format": "date-time"
                },
                {
                    "format": "date"
                }
            ],
            "serverDefault": "now",
            "title": "Date created",
            "type": "string",
            "comment": "Do not submit. The date the object is created is assigned by the server.",
            "permission": "import_items"
        },
        "submitted_by": {
            "serverDefault": "userid",
            "title": "Submitted by",
            "readonly": true,
            "rdfs:subPropertyOf": "dc:creator",
            "type": "string",
            "comment": "Do not submit. The user that created the object is assigned by the server.",
            "linkTo": "User",
            "permission": "import_items"
        },
        "notes": {
            "description": "DCC internal notes.",
            "permission": "import_items",
            "title": "Notes",
            "readonly": true,
            "type": "string",
            "comment": "Do not submit. A place for the DCC to keep information that does not have a place in the schema.",
            "pattern": "^(\\S+(\\s|\\S)*\\S+|\\S)$"
        },
        "submitter_comment": {
            "description": "Additional information specified by the submitter to be displayed as a comment on the portal.",
            "type": "string",
            "pattern": "^(\\S+(\\s|\\S)*\\S+|\\S)$",
            "title": "Submitter comment"
        },
        "documents": {
            "title": "Documents",
            "description": "Documents that describe the biosample preparation.",
            "default": [],
            "uniqueItems": true,
            "type": "array",
            "items": {
                "description": "A document that provides additional information (not data file).",
                "type": "string",
                "comment": "See document.json for available identifiers.",
                "linkTo": "Document",
                "title": "Document"
            }
        },
        "references": {
            "title": "References",
            "description": "The publications that provide more information about the object.",
            "default": [],
            "uniqueItems": true,
            "type": "array",
            "items": {
                "description": "A publication that provide smore information about the object.",
                "type": "string",
                "linkTo": "Publication",
                "title": "Reference"
            }
        },
        "source": {
            "description": "The originating lab or vendor.",
            "type": "string",
            "comment": "See source.json for available identifiers.",
            "linkTo": "Source",
            "title": "Source"
        },
        "lot_id": {
            "description": "The lot identifier provided by the originating lab or vendor.",
            "type": "string",
            "pattern": "^(\\S+(\\s|\\S)*\\S+|\\S)$|^$",
            "title": "Lot ID"
        },
        "product_id": {
            "description": "The product identifier provided by the originating lab or vendor.",
            "type": "string",
            "pattern": "^(\\S+(\\s|\\S)*\\S+|\\S)$|^$",
            "title": "Product ID"
        },
        "biosample_type": {
            "enum": [
                "primary cell",
                "immortalized cell line",
                "tissue",
                "in vitro differentiated cells",
                "induced pluripotent stem cell line",
                "whole organisms",
                "stem cell"
            ],
            "description": "The general category of the biosample.",
            "type": "string",
            "comment": "Required property. The specified category should match the type of ontology used to describe the biosample.",
            "title": "Biosample type"
        },
        "biosample_term_id": {
            "description": "Ontology identifier describing biosample.",
            "@type": "@id",
            "title": "Ontology ID",
            "type": "string",
            "comment": "For detailed description of ontologies used by DCC visit https://www.encodeproject.org/help/getting-started/. In cases where a new ontology term is needed, NTR (new term request) identifier would be provided by the DCC.",
            "pattern": "^(UBERON|EFO|CL|NTR|FBbt|WBbt):[0-9]{2,8}$"
        },
        "biosample_term_name": {
            "description": "Ontology term describing biosample.",
            "type": "string",
            "comment": "The term should match the ontology identifier specified in biosample_term_id. For detailed description of ontologies used by DCC visit https://www.encodeproject.org/help/getting-started/.",
            "title": "Ontology term"
        },
        "genetic_modifications": {
            "description": "Genetic modification(s). Any genetic alteration of a biosample or donor.",
            "items": {
                "description": "Genetic modification(s).",
                "type": "string",
                "comment": "See genetic_modification.json for available identifiers.",
                "linkTo": "GeneticModification",
                "title": "Genetic modification"
            },
            "uniqueItems": true,
            "readonly": true,
            "permission": "import_items",
            "title": "Genetic modifications",
            "type": "array",
            "comment": "Work in progress. Constructs, TALENs and RNAi objects are being migrated to objects that would be linked via genetic_modifications objects to the biosamples/donors.",
            "default": []
        },
        "alternate_accessions": {
            "permission": "import_items",
            "description": "Accessions previously assigned to objects that have been merged with this object.",
            "default": [],
            "title": "Alternate accessions",
            "readonly": true,
            "type": "array",
            "comment": "Do not submit. Only admins are allowed to set or update this value.",
            "items": {
                "title": "Alternate Accession",
                "description": "An accession previously assigned to an object that has been merged with this object.",
                "comment": "Only accessions of objects that have status equal replaced will work here.",
                "type": "string",
                "format": "accession",
                "pattern": "^(ENCBS\\d{3}[A-Z]{3})$|^(TSTBS\\d{6})$"
            }
        },
        "description": {
            "description": "A plain text description of the biosample. Do not include experiment details, constructs or treatments.",
            "title": "Description",
            "type": "string",
            "comment": "Free text description of the biosample, do not mix with biosample summary that is calculated and controlled.",
            "elasticsearch_mapping_index_type": {
                "title": "Field mapping index type",
                "description": "Defines one of three types of indexing available",
                "type": "string",
                "default": "analyzed",
                "enum": [
                    "analyzed",
                    "not_analyzed",
                    "no"
                ]
            },
            "pattern": "^(\\S+(\\s|\\S)*\\S+|\\S)$|^$"
        },
        "constructs": {
            "description": "Expression or targeting vectors stably or transiently transfected (not RNAi).",
            "default": [],
            "title": "DNA constructs",
            "uniqueItems": true,
            "type": "array",
            "comment": "A list of constructs used to transfect the biosample, it will require transfection_type specification.",
            "items": {
                "title": "DNA Constructs",
                "description": "An expression or targeting vector stably or transiently transfected (not RNAi).",
                "comment": "See construct.json for available identifiers.",
                "type": "string",
                "linkTo": "Construct"
            }
        },
        "rnais": {
            "description": "RNAi vectors stably or transiently transfected.",
            "default": [],
            "title": "RNAi vectors",
            "uniqueItems": true,
            "type": "array",
            "comment": "A list of RNAi object identifiers used to transfect the biosample, it will require transfection_type specification.",
            "items": {
                "title": "RNAi Vector",
                "description": "RNAi vector stably or transiently transfected.",
                "comment": "See rnai.json for available identifiers.",
                "type": "string",
                "linkTo": "RNAi"
            }
        },
        "treatments": {
            "description": "A list of treatments applied to the biosample.",
            "default": [],
            "title": "Treatments",
            "uniqueItems": true,
            "type": "array",
            "comment": "A list of treatments applied to the biosample, it is required to be non-empty if post_treatment_time or post_treatment_time_units are specified.",
            "items": {
                "title": "Treatment",
                "comment": "See treatment.json for available identifiers.",
                "type": "string",
                "linkTo": "Treatment"
            }
        },
        "dbxrefs": {
            "description": "Biosample identifiers from external resources, such as Biosample database or Cellosaurus.",
            "@type": "@id",
            "uniqueItems": true,
            "readonly": true,
            "rdfs:subPropertyOf": "rdfs:seeAlso",
            "permission": "import_items",
            "default": [],
            "title": "External identifiers",
            "type": "array",
            "comment": "Do not submit. DCC personnel is responsible for submission of biosample external resource identifiers.",
            "items": {
                "title": "External identifier",
                "description": "An identifier from external resource.",
                "type": "string",
                "pattern": "^((UCSC-ENCODE-cv:[\\S\\s\\d\\-\\(\\)\\+]+)|(GTEx:[a-zA-Z0-9\\-_]+)|(GEO:SAMN\\d+)|(Cellosaurus:CVCL_\\w{4}))$"
            }
        },
        "donor": {
            "description": "The donor or strain the biosample was originated from.",
            "type": "string",
            "comment": "For human biosamples, see human_donor.json for available identifiers. For mouse biosamples, see mouse_donor.json for available identifiers. For worm biosamples, see worm_donor.json for available identifiers. For fly biosamples, see fly_donor.json for available identifiers.",
            "linkTo": "Donor",
            "title": "Donor"
        },
        "organism": {
            "description": "The organism the biosample was originated from.",
            "type": "string",
            "comment": "See organism.json for available identifiers.",
            "linkTo": "Organism",
            "title": "Organism"
        },
        "passage_number": {
            "description": "Number of passages including the passages from the source.",
            "type": "integer",
            "comment": "In calculating passage number, include passages from the source.",
            "title": "Passage number"
        },
        "depleted_in_term_name": {
            "description": "UBERON (Uber Anatomy Ontology) term best matching the tissue(s)/body part(s) that were removed from the biosample.",
            "type": "array",
            "uniqueItems": true,
            "items": {
                "type": "string",
                "enum": [
                    "head",
                    "limb",
                    "salivary gland",
                    "male accessory sex gland",
                    "testis",
                    "female gonad",
                    "digestive system",
                    "arthropod fat body",
                    "antenna",
                    "adult maxillary segment",
                    "female reproductive system",
                    "male reproductive system"
                ]
            },
            "title": "Depleted in term"
        },
        "model_organism_mating_status": {
            "enum": [
                "mated",
                "virgin",
                "sterile",
                "mixed"
            ],
            "description": "The mating status of the animal.",
            "type": "string",
            "comment": "The value is not available for human biosamples.",
            "title": "Mating status"
        },
        "internal_tags": {
            "description": "Some biosamples are part of particular data collections.",
            "items": {
                "type": "string",
                "enum": [
                    "DREAM",
                    "ENCORE",
                    "ENTEx",
                    "SESCC"
                ]
            },
            "uniqueItems": true,
            "readonly": true,
            "default": [],
            "title": "Internal tags",
            "type": "array",
            "comment": "Do not submit. Internal tags are for DCC use only.",
            "permission": "import_items"
        },
        "originated_from": {
            "description": "A biosample that the sample was orginated from.",
            "type": "string",
            "comment": "See biosample.json for available identifiers.",
            "linkTo": "Biosample",
            "title": "Originated from"
        },
        "pooled_from": {
            "title": "Pooled from",
            "description": "The biosamples from which aliquots were pooled to form the biosample.",
            "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"
            },
            "uniqueItems": true,
            "type": "array",
            "comment": "A list of biosamples used to create the biosample, if specified, it requires minimum of two entries."
        },
        "part_of": {
            "description": "A biosample from which a discrete component was taken. That component is this biosample.",
            "type": "string",
            "comment": "See biosamples.json for available identifiers.",
            "linkTo": "Biosample",
            "title": "Separated from"
        },
        "host": {
            "description": "A biosample that was hosting this biosample.",
            "type": "string",
            "comment": "For example a mouse could be a host of bone marrow biosample in case of transplantation. See biosamples.json for available identifiers.",
            "linkTo": "Biosample",
            "title": "Host biosample"
        },
        "subcellular_fraction_term_name": {
            "enum": [
                "chromatin",
                "cytosol",
                "insoluble cytoplasmic fraction",
                "membrane",
                "mitochondria",
                "nuclear matrix",
                "nucleolus",
                "nucleoplasm",
                "nucleus",
                "polysome"
            ],
            "description": "The GO (Gene Ontology) term name for cellular component that constitutes the biosample.",
            "type": "string",
            "title": "Subcellular fraction name"
        },
        "phase": {
            "enum": [
                "G1",
                "G1b",
                "G2",
                "S",
                "S1",
                "S2",
                "S3",
                "S4",
                "early S",
                "late S"
            ],
            "description": "Specification of cell cycle phase of the biosample.",
            "type": "string",
            "comment": "The phase property is restricted to biosamples with biosample_type that belongs to [primary cell, immortalized cell line, in vitro differentiated cells, induced pluripotent stem cell line, stem cell].",
            "title": "Cell-cycle phase"
        },
        "transfection_type": {
            "enum": [
                "stable",
                "transient"
            ],
            "description": "The persistence of the transfection construct.",
            "type": "string",
            "comment": "transfection_type requires specification of transfection_method.",
            "title": "Transfection type"
        },
        "transfection_method": {
            "enum": [
                "electroporation",
                "transduction",
                "chemical"
            ],
            "description": "How the transfection was performed on the biosample to introduce the contruct or RNAi.",
            "type": "string",
            "comment": "transfection_method requires specification of transfection_type.",
            "title": "Transfection method"
        },
        "culture_harvest_date": {
            "format": "date",
            "description": "For cultured samples, the date the biosample was taken.",
            "type": "string",
            "comment": "Date should be submitted in as YYYY-MM-DD. The property is limited to biosamples with biosample_type that belongs to [primary cell, immortalized cell line, in vitro differentiated cells, induced pluripotent stem cell line, stem cell].",
            "title": "Culture harvest date"
        },
        "culture_start_date": {
            "format": "date",
            "description": "For cultured samples, the date the culture was started. For cell lines, the date this particular growth was started, not the date the line was established.",
            "type": "string",
            "comment": "Date should be submitted in as YYYY-MM-DD. The property is limited to biosamples with biosample_type that belongs to [primary cell, immortalized cell line, in vitro differentiated cells, induced pluripotent stem cell line, stem cell].",
            "title": "Culture start date"
        },
        "date_obtained": {
            "format": "date",
            "description": "For tissue samples, the date the biosample was taken.",
            "type": "string",
            "comment": "Date should be submitted in as YYYY-MM-DD.",
            "title": "Date obtained"
        },
        "starting_amount": {
            "minimum": 0,
            "description": "The initial quantity of cells, tissue or animals obtained.",
            "type": "number",
            "title": "Starting amount"
        },
        "starting_amount_units": {
            "enum": [
                "g",
                "mg",
                "cells/ml",
                "cells",
                "whole embryos",
                "items",
                "μg",
                "whole animals"
            ],
            "description": "The units used to quantify the amount of cells or tissue obtained.",
            "type": "string",
            "title": "Starting amount units"
        },
        "url": {
            "description": "An external resource with additional information about the biosample.",
            "type": "string",
            "format": "uri",
            "title": "URL"
        },
        "model_organism_sex": {
            "enum": [
                "male",
                "female",
                "unknown",
                "mixed",
                "hermaphrodite"
            ],
            "description": "The sex of the organism the biosample comes from.",
            "type": "string",
            "comment": "model_organism_sex is not valid for a human biosample.",
            "title": "Model organism sex"
        },
        "mouse_life_stage": {
            "enum": [
                "adult",
                "unknown",
                "embryonic",
                "postnatal"
            ],
            "description": "The life stage of the mouse biosample.",
            "type": "string",
            "comment": "mouse_life_stage is not valid for a human biosample.",
            "title": "Mouse life stage"
        },
        "fly_life_stage": {
            "enum": [
                "embryonic",
                "larva",
                "first instar larva",
                "second instar larva",
                "third instar larva",
                "wandering third instar larva",
                "prepupa",
                "pupa",
                "adult"
            ],
            "description": "Fly development stage of the animals used to prepare the biosample.",
            "type": "string",
            "comment": "fly_life_stage is valid only for fly biosamples.",
            "title": "Fly life stage"
        },
        "fly_synchronization_stage": {
            "enum": [
                "fertilization",
                "egg laying",
                "first larval molt",
                "second larval molt",
                "puff stage: PS (1-2), dark blue gut",
                "puff stage: PS (3-6), light blue gut",
                "puff stage: PS (7-9), clear gut",
                "white prepupa",
                "eclosion"
            ],
            "description": "Fly development stage at which flies were synchronized.",
            "type": "string",
            "comment": "Stage at which flies were synchronized. If available use in conjunction with time and time units post-synchronization.",
            "title": "Fly synchronization stage"
        },
        "post_synchronization_time": {
            "description": "The time that elapsed past the point when animals were synchronized.",
            "type": "string",
            "comment": "Use in conjunction with fly_synchronization_stage or worm_synchronization_stage to specify time elapsed post-synchronization. It requires specification of post_synchronization_time_units as well.",
            "pattern": "^(\\d+(\\.[1-9])?(\\-\\d+(\\.[1-9])?)?)|(unknown)$",
            "title": "Post-synchronization time"
        },
        "post_synchronization_time_units": {
            "enum": [
                "minute",
                "hour",
                "day",
                "week",
                "month",
                "stage"
            ],
            "description": "The units of time that elapsed past the point when animals were synchronized.",
            "type": "string",
            "comment": "Use in conjunction with fly_synchronization_stage or worm_synchronization_stage and post_synchronization_time to specify time elapsed post-synchronization.",
            "title": "Post-synchronization time units"
        },
        "post_treatment_time": {
            "description": "The time that elapsed past the point when biosamples were treated.",
            "type": "string",
            "comment": "Use in conjunction with treatment and post_treatment_time_units to specify time elapsed post-treatment. post_treatment_time specification requires non-empty treatments list and post_treatment_time_units specification.",
            "pattern": "^(\\d+(\\.[1-9])?(\\-\\d+(\\.[1-9])?)?)|(unknown)$",
            "title": "Post-treatment time"
        },
        "post_treatment_time_units": {
            "enum": [
                "minute",
                "hour",
                "day",
                "week",
                "month",
                "stage"
            ],
            "description": "The units of time that elapsed past the point when biosamples were treated.",
            "type": "string",
            "comment": "Use in conjunction with post_treatment_time and treatment to specify time elapsed post-treatment. post_treatment_time_units specification requires non-empty treatments list and post_treatment_time specification.",
            "title": "Post-treatment time units"
        },
        "worm_life_stage": {
            "enum": [
                "early embryonic",
                "midembryonic",
                "late embryonic",
                "mixed stage",
                "mixed stage (embryonic)",
                "mixed stage (late embryonic and L1 larva)",
                "L1 larva",
                "L2 larva",
                "L2d larva",
                "L3 larva",
                "L4 larva",
                "dauer",
                "L4/young adult",
                "young adult",
                "adult"
            ],
            "description": "Worm development stage of the animals used to prepare the biosample.",
            "type": "string",
            "comment": "worm_life_stage is valid only for worm biosamples.",
            "title": "Worm life stage"
        },
        "worm_synchronization_stage": {
            "enum": [
                "fertilization",
                "egg laying",
                "egg bleaching",
                "4 cell",
                "L1 larva starved after bleaching",
                "dauer exit"
            ],
            "description": "Worm development stage at which the animals were synchronized.",
            "type": "string",
            "comment": "Stage at which worms were synchronized. Use in conjunction with time and time units post-synchronization.  worm_life_stage is valid only for worm biosamples.",
            "title": "Worm synchronization stage"
        },
        "model_organism_age": {
            "description": " The age or age range of the model donor organism when biological material was sampled.",
            "type": "string",
            "comment": "model_organism_age is not valid for a human biosample.",
            "pattern": "^((\\d+(\\.\\d+)?(\\-\\d+(\\.\\d+)?)?)|(unknown))$",
            "title": "Model organism donor age"
        },
        "model_organism_age_units": {
            "enum": [
                "minute",
                "hour",
                "day",
                "week",
                "month",
                "year",
                "stage"
            ],
            "description": "Age units of the model organism.",
            "type": "string",
            "comment": "model_organism_age_units are not valid for a human biosample.",
            "title": "Model organism donor age units"
        },
        "model_organism_health_status": {
            "description": "Health status of the model organism.",
            "type": "string",
            "comment": "model_organism_health_status is not valid for a human biosample.",
            "title": "Model organism donor health status"
        },
        "@type": {
            "type": "array",
            "items": {
                "type": "string"
            },
            "calculatedProperty": true,
            "title": "Type"
        },
        "parent_of": {
            "description": "The biosample(s) that have this biosample in their part_of property.",
            "type": "array",
            "comment": "Do not submit. Values in the list are reverse links of a biosamples that are part_of this biosample.",
            "items": {
                "linkFrom": "Biosample.part_of",
                "type": [
                    "string",
                    "object"
                ]
            },
            "title": "Child biosamples"
        },
        "organ_slims": {
            "type": "array",
            "items": {
                "type": "string"
            },
            "calculatedProperty": true,
            "title": "Organ slims"
        },
        "health_status": {
            "type": "string",
            "calculatedProperty": true,
            "title": "Health status"
        },
        "subcellular_fraction_term_id": {
            "type": "string",
            "calculatedProperty": true,
            "title": "subcellular_fraction_term_id"
        },
        "characterizations": {
            "type": "array",
            "items": {
                "linkFrom": "BiosampleCharacterization.characterizes",
                "type": [
                    "string",
                    "object"
                ]
            },
            "title": "Characterizations"
        },
        "@id": {
            "type": "string",
            "calculatedProperty": true,
            "title": "ID"
        },
        "synchronization": {
            "type": "string",
            "calculatedProperty": true,
            "title": "Synchronization"
        },
        "summary": {
            "type": "string",
            "calculatedProperty": true,
            "title": "Summary"
        },
        "age_display": {
            "type": "string",
            "calculatedProperty": true,
            "title": "Age"
        },
        "age": {
            "type": "string",
            "calculatedProperty": true,
            "title": "Age"
        },
        "system_slims": {
            "type": "array",
            "items": {
                "type": "string"
            },
            "calculatedProperty": true,
            "title": "System slims"
        },
        "depleted_in_term_id": {
            "type": "string",
            "calculatedProperty": true,
            "title": "depleted_in_term_id"
        },
        "life_stage": {
            "type": "string",
            "calculatedProperty": true,
            "title": "Life stage"
        },
        "biosample_synonyms": {
            "type": "array",
            "items": {
                "type": "string"
            },
            "calculatedProperty": true,
            "title": "Biosample synonyms"
        },
        "model_organism_donor_constructs": {
            "description": "Expression or targeting vectors stably or transiently transfected (not RNAi) into a donor organism.",
            "type": "array",
            "items": {
                "description": "An expression or targeting vector stably or transiently transfected (not RNAi) into a donor organism.",
                "type": "string",
                "comment": "See contstruct.json for available identifiers.",
                "linkTo": "Construct",
                "title": "DNA Constructs"
            },
            "calculatedProperty": true,
            "title": "DNA constructs"
        },
        "age_units": {
            "type": "string",
            "calculatedProperty": true,
            "title": "Age units"
        },
        "developmental_slims": {
            "type": "array",
            "items": {
                "type": "string"
            },
            "calculatedProperty": true,
            "title": "Developmental slims"
        },
        "sex": {
            "type": "string",
            "calculatedProperty": true,
            "title": "Sex"
        }
    },
    "facets": {
        "organism.scientific_name": {
            "title": "Organism"
        },
        "status": {
            "title": "Biosample status"
        },
        "biosample_type": {
            "title": "Biosample type"
        },
        "organ_slims": {
            "title": "Organ"
        },
        "sex": {
            "title": "Sex"
        },
        "life_stage": {
            "title": "Life stage"
        },
        "subcellular_fraction_term_name": {
            "title": "Subcellular fraction"
        },
        "phase": {
            "title": "Cell cycle phase"
        },
        "treatments.treatment_term_name": {
            "title": "Biosample treatment"
        },
        "transfection_type": {
            "title": "Transfection type"
        },
        "transfection_method": {
            "title": "Transfection method"
        },
        "source.title": {
            "title": "Source"
        },
        "lab.title": {
            "title": "Lab"
        },
        "award.project": {
            "title": "Project"
        },
        "award.rfa": {
            "title": "RFA"
        }
    },
    "columns": {
        "accession": {
            "title": "Accession"
        },
        "description": {
            "title": "Description"
        },
        "age": {
            "title": "Age"
        },
        "age_units": {
            "title": "Age Units"
        },
        "biosample_term_name": {
            "title": "Term"
        },
        "biosample_type": {
            "title": "Type"
        },
        "synchronization": {
            "title": "Synchronization"
        },
        "post_synchronization_time": {
            "title": "Post-synchronization time"
        },
        "post_synchronization_time_units": {
            "title": "Post-synchronization time units"
        },
        "organism.scientific_name": {
            "title": "Species"
        },
        "source.title": {
            "title": "Source"
        },
        "lab.title": {
            "title": "Submitter"
        },
        "life_stage": {
            "title": "Life stage"
        },
        "status": {
            "title": "Status"
        },
        "rnais.target.label": {
            "title": "RNAi target"
        },
        "treatments.treatment_term_name": {
            "title": "Treatment"
        },
        "constructs.target.label": {
            "title": "Construct"
        },
        "culture_harvest_date": {
            "title": "Culture harvest date"
        },
        "date_obtained": {
            "title": "Date obtained"
        },
        "model_organism_donor_constructs.target.label": {
            "title": "Constructs"
        },
        "donor.mutated_gene.label": {
            "title": "Mutated gene"
        },
        "treatments.length": {
            "title": "Treatments length"
        },
        "constructs.length": {
            "title": "Constructs"
        },
        "summary": {
            "title": "Summary"
        },
        "summary_object": {
            "title": "Summary object"
        }
    },
    "boost_values": {
        "accession": 1,
        "aliases": 1,
        "alternate_accessions": 1,
        "biosample_term_id": 1,
        "biosample_term_name": 1,
        "organ_slims": 1,
        "developmental_slims": 1,
        "biosample_synonyms": 1,
        "dbxrefs": 1,
        "subcellular_fraction_term_name": 1,
        "phase": 2,
        "life_stage": 1,
        "synchronization": 1,
        "health_status": 1,
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