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,
"donor.accession": 1,
"donor.alternate_accessions": 1,
"donor.organism.name": 1,
"donor.organism.scientific_name": 1,
"donor.organism.taxon_id": 1,
"award.title": 1,
"award.project": 1,
"submitted_by.email": 1,
"submitted_by.first_name": 1,
"submitted_by.last_name": 1,
"lab.institute_name": 1,
"lab.institute_label": 1,
"lab.title": 1,
"source.title": 1,
"treatments.treatment_type": 1,
"treatments.treatment_term_id": 1,
"treatments.treatment_term_name": 1,
"treatments.dbxrefs": 1,
"treatments.aliases": 1,
"constructs.construct_type": 1,
"constructs.vector_backbone_name": 1,
"constructs.target.gene_name": 1,
"constructs.target.label": 1,
"constructs.target.dbxref": 1,
"constructs.target.aliases": 1,
"originated_from.accession": 1,
"originated_from.alternate_accessions": 1,
"originated_from.biosample_term_id": 1,
"originated_from.biosample_term_name": 1,
"pooled_from.accession": 1,
"pooled_from.alternate_accessions": 1,
"pooled_from.biosample_term_id": 1,
"pooled_from.biosample_term_name": 1,
"characterizations.characterization_method": 1,
"rnais.rnai_type": 1,
"rnais.vector_backbone_name": 1,
"rnais.target.organism.name": 1,
"rnais.target.organism.scientific_name": 1,
"rnais.target.organism.taxon_id": 1,
"rnais.source.title": 1,
"organism.name": 1,
"organism.scientific_name": 1,
"organism.taxon_id": 1,
"references.title": 1,
"rnais.product_id": 1,
"rnais.target.label": 1,
"rnais.target.aliases": 1,
"award.pi.title": 1,
"notes": 1,
"internal_tags": 1
},
"changelog": "/profiles/changelogs/biosample.md",
"@type": [
"JSONSchema"
]
}